Since the derailleur and chain sit so low on the 20" rear wheel, the chain will rub the front roller when some gear combinations are used. On some gear combinations, there is only an inch or two of clearance between the chain and ground. The minimual clearance has never been a problem when riding on real roads.
-----Question 1: How far apart should the rollers be set?
-----Question 2: Is just one gear used on a trainer? What is the proper way to ride on a trainer?
Rans Screamer, Catrike Expedition, Specialized Montain Bike, Cannondale Quick SL1
These are all great questions. I have my Catrike on an old Norco trainer, a single barrel on the rear wheel. But to adapt the unit for 20" wheels, I had to raise the roller. To "level" everything out, I placed 6x6 posts under the two front wheels. Chain and derailleur clearance is not an issue; everything looks and feels (and sounds) just like I'm on the road. The trike "walks" a little as I ride so it's necessary to realign everything every 30 minutes or so. I use any and all gears, and spin away to my heart's content. (Read HRM) With a good cadence, in 40 minutes, I'm a puddle! Good luck.
I think mchell has it right. You need to block up the front wheels to level the trike. You can make your own or buy them. Ideally, you want them to be the same height as the rear wheel as it sits between the rollers. In their simplest form, they could be 2x4s, but they would work better if you made something a little more elaborate, with ridges around the wheel slots and a wider base for stability.