Cherry pits require a period of cold dormancy of atleast 2 months, but are better off and more likely to germinate with 3-4 months (I just stick them in my fridge). They should have a decent rate of germination, but I would do quite a few just in case, and if nothing else, you can give them away if you have to many.
I don't know about rootstock as I've never bothered trying it, but you could go for a quasi-bonsai sort of thing. Get yourself some big pots (wiskey barrels would probably work) and plant them in there. Then, treat them kind of like big bonsai, pruning roots and branches as need be, monitoring soil and fertilizer needs, etc for the pots and soil they are in. They should be able to grow for several years without much pruning or special attention, however eventually you will want to so that they don't outgrow the pots. If you prune roots and branches though (mostly its the roots that do it), it will dwarf the trees and they will still flower. However, be aware that of course you cannot predict the sex of a tree, so if you just keep two seedlings, you will not know for quite a while whether they are male or female, and you may end up with two girls (sounds like you already have atleast one).