Jet,
I have the Andy Low ECU and I am running Dualities so charging is different but I would disconnect it anyway any time you’re not flying the plane. I have found with mine that it seems to draw a small amount of power from the battery even when the system is off.
I found that if I charged all the batteries in the plane and then left it set for a week or so when I went to top off the batteries the ECU battery would be almost dead and the RX's were fine. So I started disconnecting it from the ECU and it was fine from then on.

Also just an FYI if you use LIPO's you will have to regulate to 6V at the ECU or you will get a very cool after burner. Andy's ECU's use the volts to regulate the pump and the extra volts of the LIPO's caused a little (well a lot) of extra fuel to flow. I tested it on the stand and got about a 2 foot + flame out the back for a few seconds till I shut it down.

Dave