Probably just doing what I am doing, though I know others may have great ideas I wouldn't think of.
1) Use a different bedding type for the litter box than for the rest of the cage and remain consistent with your choice. When getting new rats, if you have contact with a rat's former owner/breeder/rescuer and they used litter boxes, it's good to ask them what they use.
2) Look for where they seem to be going the most. If you can figure that out, then put a litter box in that location, preferably adding some of their raisins to the litter so it smells like their potty spot.
3) Rats tend to potty at the bottom of ramps and in corners. Those are prime spots for litter boxes. Often I'll place the litter boxes with the ramp ladder actually terminating /in/ the litter box.
4) Increase chances of success. If your cage has multiple levels, get more than one litter box. I use two in my Critter Nation. I like the following because they have a high back which prevents rats from spraying urine kicking litter out of the cage, and it attaches to the cage bars preventing them from knocking it over: http://www.amazon.com/dp/B0002ASBAY/?tag=picc-20
5) Don't be afraid of creative rearranging. The nekkids were pooping all over a corner which wouldn't accommodate a litter box. I added an igloo to that corner, and they quit using it.
6) Clean up stray poops quickly and regularly, and wipe down the cage daily. This keeps the 'poop area' smell more concentrated in the litter box, also increasing the quickness of their successful training.
They should take to it pretty quickly. Earlier this week, the nekkids (and the others to a lesser degree) were pooping all over the bottom level. I added a litter box at the bottom of the ramp two days ago and my clean up on that level went from 40-90 raisins a day, to about 10. You won't get perfection, but you'll get a vast improvement.
Once they are potty trained, you can take a box out during play time and put it in the spot they try to go. They'll use it over pooping on the floor most every time. You'll find that except in cases of fear or excitement pooping, they'll be better outside of the cage.