I don't use an automated processor; however, whenever I use a wetting agent (for B&W) or final rinse/stabilizer (for C-41 or E-6), I do not agitate that last step. When I first began with my own processing, I did agitate during that step, but I found that the result was a lot of suds and a very hard time preventing streaks from forming on the negatives. Instead of agitating, I just pour in the wetting agent/final rinse/stabilizer, rap the tank a few times on the table to dislodge air bubbles, and let it sit for the recommended time. If I were using an automated processor, I imagine I'd do something similar.
Concerning kits and capacities, if your kit has greater capacity for bleach and fixer than for developer, you could always just buy developer separately between each kit purchase to maximize overall capacity. Since the developer is the item that's likely to go bad most quickly, this seems like a sensible approach to me.