AVR-Chat

>
>Would this be the way to go or are there other possibilities?

It works nicely. Remember to ramp down as well, you can't stop a motor 
instantly unless it's running very slowly.

You may find that you need more timers, but you can share timers to a degree.
I use T0 (because it's relatively dumb) for my 1mS opsys tick, that runs a 
bunch of Dec-to-zero timers for different tasks. You might be able to do a 
similar thing, depending on your other needs.