I try to use the Carter method of flattening while sharpening, but I guess that will never get you a perfectly flat stone. I know a lot of the much-more-serious-than-I sharpeners swear by these things, so I'm considering checking it out. Do you use the base when flattening the stone or just hold the insert/pad?
You use the base also. The replacement surface is just a new set of abrasives to go on your base. You won't have to get a replacement very often unless you flatten your stones very frequently or do repair work with it.