this 'advice' won't really be directed at the trainer use per se, but:

i just dealt with IT band woes this time last year, and ended up doing physical therapy from december through february of this year. at the peak of the problem, before it was diagnosed and i started PT, i could ride maybe an hour pain free, then straight to excruciating. after physical therapy sessions and regular stretching, core exercises, rolling out legs, etc. (not to mention practically zero riding from december to february), i managed to ride a metric in april, a century in june, and my first 200k in september. the take-home message i got from PT was that it was extremely important to stretch and keep your IT band (and other leg muscles/tendons/etc.) loose. simply resting won't resolve the problem at hand, you need to actively stay on top of it. core exercises were for strengthening your core and lowering the stress and demand on your legs/knees for things like balance...your legs should only be used for forward motion. a plethora of leg stretches to keep everything limber....

even though the june century was pain-free, from miles 75-95 or so of the 200k, my knee/IT band pain crept back up. i blame the elevation (~10,000ft) causing sloppy pedaling technique, but the fact that it came back always lingers in the back of my mind, as i'd like to try my hand at 300 and 400k's this coming year, but am hesitant.

i'm beginning to ramble, but what i do whenever my pain comes back up is to get on the trainer for 5-10 minutes to warm up, and then do my battery of stretches and core/leg exercises. i used to do it religiously while i was doing PT as well as after, which i think helped me significantly in getting back on the bike and being able to complete these longer distances. (my doctor, when he first diagnosed my IT band problem, said it might be a thing that would limit me to 20-30 miles a ride for the rest of my life, so glad he was wrong!).

don't just rest, but try to get to the root of the problem. figure out what's wrong, and do what needs to be done so that you don't have to deal with any pain (or at the very least, much less than what you're dealing with that will make the 600k/1000k bearable). getting more miles in on the trainer isn't necessarily going to help directly: you're still doing the same knee-bending circular motion that rubs and causes trouble over, and over, and over...... if anything, you're just building up your tolerance to the pain.