It may be simpler to separate them in breeder nets or breeder boxes. That way, no worries about ammonia or filtration or anything. You can get small nets, hang over the tank edge, or small boxes that float, both work.
Very small tanks as you are thinking of are going to be hell to manage, I've seen a few attempts at similar concepts and problems arise with keeping the water circulating and food from building up, and sometimes oxygen saturation too.
I am not certain when guppies reach sexual maturity, but I think it is not 'til after you can see some colour on the boys. So you should have some time to work with a given brood.
I keep Endlers, pure strain, and the fry are all in a large hang on inside tank breeder box, that has it's own sponge and filtration. Works very well, but of course, I can't get separate the boys out 'til they begin to show some colour. Usually shows in the tail first. I don't know how soon after that they become sexually capable, but then, the females have to be of age too.