Hi Kevin,
I would NEVER turn off helium low (or carrier in general), this is one of the worst things you can do to a GC or GCMS instrument. I ould go into a littany of reasons why, but believe me, it's bad.
Thermo uses the Gas Saver option in the method to turn down the total flow after the injection is made, you can usually find this option in the Carrier or Inlet setup tabs of the instrument method. By default the hardware will be in this "saving" state until it gets a trigger to prepare for the next injections, so relax, you don't really have to do anything, you're already saving gas. If, however, you really want to maximize the savings for a long-term standby, simply set the column flow to ~0.5mL/min and leave the inlet temp at 225°C. The inlets and detectors are much more stable and clean when left hot and inert. Same thing for the mass specs, just leave the transfer line hot and the ion source hot and obviously keep the MS on. I promise you, the instruments will be much more stable, clean and healthy doing this rather than a shutdown.
-Mark