Allow me to help ease many of your troubles by directing you to the Jade Regent GM Reference message boards.
Spend some time reading through some of the posts. There's a lot of info on the caravan system (spoiler alert: it's incredibly broken and you'll need to apply houserules to make it function. Seriously, the dev team came right out and said they never tested it and acknowledged it doesn't work.)
I skipped the caravan rules when I ran Jade Regent. Instead, when bandits or ogres attacked the caravan, I split the raiders into two groups: those who fought the party and those who fought the caravan guards. The raiders who fought the caravan guards would be out of sight and their degree of success matched the party's degree of success against their group.
I had run Rise of the Runelords and learned the time to travel around Varisa from experience. I have maps in my copies of Inner Sea World Guide and Varisa, Birthplace of Legends. If I recall correctly, I decided that the journey from Sandpoint to Riddleport took six weeks. Instead of packing supplies, send some party members out hunting via Survival skill and scouting via Perception skill (good scouting forewarns of bandits). They can keep the caravan supplied as long as necessary.