final chest <- relay <- wooden pipe with redstone engine or aut. gate <- ACT
final chest has a cobblestone pipe with a gate: if chest has space, emit redstone signal. Connect that signal to your engine or gate to start pumping. The relay is a small buffer, auto outputting if space available, thus the two or so cells that get produced each time until the engine gets shut down again won't spill.
There are no relays in the beta pack unfortunately, however I think it could be done with a BC gate on its own I think - the "if inv has space" setting. Been avoiding using these due to all the hassle needed to make them, and the stuff to make the stuff to make them too! Let me know if I'm wrong about the gate as I haven't used them and know very little about them except what I've seen in a few YT vids.