I like to leave my system powered up so it keeps satellites acquired and corrections updated. However; the EZ-Steer T2 box is very sensitive to even brief periods of low voltage and the lightbar will occasionally get flaky if it experiences a voltage sag too. My Spray-Coupe has a large enough battery and a small enough engine that it does fine being left powered on while the engine is being started. That's not the case with my combine so you may need to consider something along the lines of what I did. Small sealed 12V AGM battery and diode was less than $25 and it keeps the GPS voltage isolated from short term droops in the rest of the machine electrical supply.

http://talk.newagtalk.com/forums/thread-view.asp?tid=180662&mid=1311028#M1311028