1. Aim a level emitter at a precision export bus that's exporting into an inventory on the ME system, or use an ME interface.
2. Set the level emitter to emit a redstone signal if cobblestone is > 128. (or set it to whatever you like)
3. Set the Export bus to "craft only" and put the condensed cobblestone as the target being exported. Make sure you set the bus to "active WITH redstone signal"
4. Make a condensed cobblestone pattern and make sure its in your Molecular Assembly Chamber.
The level emitter sends a signal to the export bus when you have >128 cobble, which forces your system to craft condensed cobble only if there's excess. Be careful, setting the export bus to "move single items / craft" may cause a loop of condensed cobble being taken out and re-injected into your system...which is a waste of power.
Hope this helps!
-CaptainJack
TheMindCrafters