This article is a discussion of logistics in C4, where I live. Logistics in other parts of wspace is similar, though easier in many cases. I have lived in a C1/hs (logistics was easy there, at least as far as getting to highsec), a C4/C3, a C4/C4, and now a C4/C4+C5. I have no experience of living in C5 or C6.
There are many small and valuable goods that enter and leave wspace. Most particularly, blue loot and sleeper salvage leave. These can be carried in almost any ship, although small and fast, and cloaky, is better. A blockade runner fit for agility and speed is good for this. Since Hyperion, cloaky ships never appear within decloak range of the wormhole, so they are safer to move goods in than before.
What about larger goods? These won't fit in a blockade runner in large amounts. Here, we have to use ships with substantial cargo capacity. These ships can be caught, so they need to be used properly.
In upper wspace (C5 and C6), you can bring a freighter directly in if coming direct from known space. I have not lived in upper wspace, but this is what I think I would aim to do. One freighter with full cargohold expansion can carry over 1.1 million m^3 cargo, which is roughly 17 times what the next-largest carrier holds. It's probably worth waiting for that rare highsec connection. Support your freighter with webbing to speed it into warp.
Recon and Surveillance
You must always scan to get out of wspace, even if it is just a static highsec. So, that is the first thing to do. In deeper wspace, scanning a way out can take substantial time. It helps if you have hunters in your corp, since scanning to hunt and scanning to find paths out are very similar.
Highsec exits are preferred. However, it is possible to use lowsec as well. A lowsec system adjacent to highsec is fine if it is largely abandoned. You can count the people in local to get an idea of how busy it is.
Generally, you want as short of a path as you can get. Often my paths are two wormhole jumps, typically going through a C2/hs+C4 that has connected to my system. Sometimes we will do three hops. Longer paths than that are unnecessarily dangerous; you'll get a path of length two or three soon enough.
It's nice to have a relatively short trip to Jita. (I am using Jita as your assumed highsec base, where you have a freighter and an alt to drive it. This is how I do it.) Remember that a freighter takes 3 minutes per jump when piloted, and more like five per jump on autopilot (and also that autopiloting in highsec is relatively dangerous, especially through Uedama and Niarja). And that is if you leave immediately; if you need time to put together stuff to bring, it will be longer. Running stuff in and out of wspace will also take time. Schedule to the playtime you have.
When a scout does exit out into highsec and finds a good route, he should bookmark the nearest station in the system. (We call it "nearby - stationstring", where stationstring is the string that is put into the bookmark by default when you select the station and make a bookmark.) If there are no stations in the exit system, or it is lowsec, the scout should go one hop towards Jita and bookmark the nearest station to that gate. The nearby station is the station that your freighter pilot will fly to, and also pilots carrying goods down out of wspace. Goods are passed between them by station trading (if they are there simultaneously, which is typical), or by contract.
When you have found a nice short path out to highsec (or sometimes lowsec), it's time to reconnoiter it. You'll want a look at each system in the path, and also each adjacent system. Is there anyone in the systems in the path? No? OK, proceed. Yes? Probably not a good time to run logistics.
Is there anyone in any adjacent systems? No? Then go ahead. Yes? Be cautious. At minimum you'll want to keep a sound picket on the wormhole between them and your path. If you can't do that, it's probably too dangerous.
Once you've decided to run goods, it's time to bring the freighter out from Jita. This can take time. While the freighter crawls across highsec, you should monitor the system(s) in the path as much as you can. Any probes are a bad sign, although scouts will tend to move on. Don't leave your probes out where anyone can see them and get interested. Don't move lots of ships except as below. Don't do anything to attract attention to your path.
Escorts and Eyes
Before running goods, get escorts ready in the path. And get on coms. Falcons are the ideal ship for the job, but you can use any cloaky.
The primary job of the escort is simply to alert people if he sees anything. He should sit in a system near (15 km off of) one wormhole in the path, and ideally have dscan surveillance over any live towers and/or the other wormhole. If there is substantial traffic in anything larger than an unarmed frigate, you should consider scratching the logistics attempt. There will be another day.
The secondary job of the escort is a last-ditch attempt to save your transports by jamming out attackers. (That's why Falcon.) However, it is risky and very undesirable to rely on this. If you suspect attack, it's better to just not do logistics.
Ideally, you should have at least one escort for each dangerous system you are moving goods through. For example, if the path is C4a->C2a->hs, use two escorts -- one in C4a, the other in C2a. You can run with fewers escorts (or indeed, none), but it is is riskier. If you have to leave systems unwatched, it should be your home system, systems with no live towers, systems with occupants who play at other times, and/or systems with few wormholes except the two directly in the pipe you are using.
Once the freighter is getting close, you may want to send out your first loads of bulky stuff. PI goods can be done in Epithals, particularly if there are also PI goods to come in. All goods can go in DSTs. Try to carry out your most valuable stuff first, because the risk of attack will increase with the more runs you make. This is your first run; it's the least predictable.
Transports should move as a group; that is, a convoy. Being in a convoy will get them ganked as a group if you are unlucky enough to get bubbled and multiply-pointed. However, that is extremely rare if your escorts are paying attention. More likely is an attack by a lone bomber or T3 hunter. Here, the convoy makes sure most of the goods get through.
Escorts should make sure each system in the path is clear before transports jump in. Both wormholes must be clear to proceed. You can see if a remote location is clear on dscan if it is within 14.3 AU: it is not clear if there are any ships there of any kind, and/or if there is a bubble there. If the other wormhole is out of dscan range, warp over there (at 30km), and check.
Transports should meet up with the freighter at the nearby station for goods transfer. Be ready to turn around promptly. Wait out polarization in highsec. I usually don't wait out polarization in wspace because any attacker will just cross-jump to get you anyway.
If you do get attacked, then you'll have to figure how to proceed. A small attack (i.e. one stealth bomber) can sometimes simply be run by. Epithals and DSTs should be heavily warp core stabilized. If the attack is larger, getting by safely becomes less likely. DSTs may be able to micro jump past bubbles; others will have to turn back. Falcons can assist here by jamming out the ships pointing the DSTs. If you do get attacked, don't try to keep moving. Wspace hunters are like sharks. Let them get bored. Don't run any logistics at least an hour. Make sure to log off your characters or cloak them up; leaving them sitting at a POS is too visible and will keep hope alive.
When transports have just passed through a system, and you are planning more passes through there, the escorts there should be particularly alert. (I.e.: dscan more.) You are looking for any change, which would tend to indicate that someone saw your run and is getting ready to ambush.