Use the round bases, and use regular square movement trays. If you're using plastic models, you really don't need magnets, although they do make them more secure.
I do recommend using rare earth magnets and lining the bottoms of your movement trays with a thin sheet of steel, though. It's really quite easy and makes moving and storing the unit wonderfully convenient. You can just put the whole unit away on their movement tray in a case (several friends of mine just use cheap toolboxes from walmart or where ever), rather than having to pack and unpack all the individual models. It's awesomely convenient for very little upfront investment of work.
There are very few models this doesn't work for; those you can either give swappable bases, or just dedicate them to one game system or the other.
Edit: Hey, you're in Charlottesville! That's where I played my first Warhammer Fantasy GT! The Colonial, back in 2005! Blast from the past. Good times.
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