You'll probably want to germinate in small containers, which work fine when bottom fed. I use styrofoam cups that are placed on top of a capillary mat, which draws water from a container underneath. Works great, keepz the soil moist but not wet. I have these in my indoor seed starter; it has temperature controls and fans to keep young plants moving. Works great for mint, tomatoes and peppers. Peppers actually like to be 'abused' a bit - periods of drought, hard winds, large variation in temperature. Makes them very bushy with thick stems. With a computerized system this is easy to implement, but the problem is how to measure the response variable in such a system (or even define it) to set up a fully self-regulating system. The hard- and software in these systems are easy, it's the botany, biochemistry and horticulture that is hard.