I'm using a M11 that I have recently fitted a lipo into. As I'm not going to be using it over the next few months I'm sure I need to put the lipo into storage mode. However, will my M11 lose it's settings or should I put AA's in just for the down time?

It will be fine, When I had my M11 I would unplug my lipo after racedays and take the summer off, never any problems with settings.

That's correct,settings will remain the same.

All your settings are stored on a chip and a battery (or lack of) will have no impact on those settings.