I'm also having a little issue with the logistics of the caravan. Since my players opted to have their PCs all hire out separately, they are going to be all spread out during the journey. I'm struggling to see how to make some of the encounters on the road work so that all the PCs can be involved.
All of my PCs hired out separately as well, but it didn't cause serious problems. Which specific encounters are you worried about?
I had some tips for running the caravan in
this post and
this one. Of those, I'd stress making sure that there are colorful NPCs working alongside the PCs in each of their separate wagons. (If you don't have anyone placed already, remember that new people can join the caravan at any small town or wayhouse.) Some examples that I used:
1. Radecere, the gambling gnome, was a passenger on one of the PCs' wagons. He would always try to get anyone near him to bet on anything he could think of. This resulted in him getting into debt to our Cleric for 50 gp; the Cleric then made him work off the debt by calling in favors, until Radecere finally borrowed enough from Jamna Gleamsilver to pay the Cleric off.
2. The Wizard's wagon had a mysterious passenger who never came out and was heavily cloaked and hooded any time the door was open; it was, of course, Green Imsa.
3. Sulesdeg the Pole worked on a wagon alongside our Battlemaster. I described him as being super-hot in addition to his height, although not very talkative, but they bonded a bit over both being from desert areas--the Battlemaster is from Calimshan originally. She was disappointed when the Wizard convinced Sulesdeg to leave the caravan.
The main difficulty for me with the PCs split up on different wagons was "Adventuring Life." I handled that by making it so the PCs were not the ones to get fired; instead, their friend Orvustia (who had a crush on the Eldritch Knight, which was causing tension between him and the Battlemaster) was the one to lose her job. She came to them in tears, and they had to find her a new position. The Eldritch Knight let her take over his job, which then freed him to join the Battlemaster's wagon.
And the logical part of my brain is telling me that some of the more experienced NPC guards would reasonably get involved in some of them - like the peryton attack, for instance - but that'll really slow things down at the table and also potentially make the encounters too easy.
I had the same thought. Depending on the encounter, I handled it various ways. For some ("Stranded," for instance), I said that there were actually a lot more attackers than were on the map; the other caravan guards were fighting "offscreen," and I was only focusing on the portion that the PCs were involved in. For others, like "Bane of the Mountains" or "Spider Woods," I told the PCs that their wagons happened to be bunched up in the caravan order and the perytons/ettercaps just happened to attack that part of the line. For "Fungus Humungous," having separate wagons actually made it more interesting, as it meant each PC had to come up with a separate solution. And for "No Room in the Inn," I just had the caravan leader report that the inn was unavailable; the PCs then volunteered to go check it out, but if they hadn't, I'd have prodded them with NPCs.
Hope this helps!