This seems like a frequent question, so I thought I'd share my current solution. This system is designed so that can burst a section of storage to mass fabrication while always keeping a reserve so that power from always-on sources isn't wasted. It should be easily modifiable to any number of storage devices.
Power comes in to the MFSU on the left, and fills both. They're both set to "Emit when full." When they're both full at the same time, the AND gate triggers the RS latch to reverse it's outputs, which allows the mass fab to run, and cuts the right-hand MFSU off from additional power input. When it's empty the shutoff of the detector cable triggers the pulse former to reverse the RS latch again, disabling the MF, and allowing the second MFSU to charge again.
The cables going down through the floor supply power everything else, and allow the rest of the equipment to use power from either MFSU regardless of what the system is doing. They need to have separate MFTFs, so that power can't bypass the splitter cable.
If you have scrap available (I don't, here) you can connect the same redwire line that controls the MF to a RedPower timer that sends scrap while the MF is running.