"Master mode" is used in several different contexts in Falcon, but it most often refers to the master mode of the Fire Control Computer (FCC), which is sometimes referred to as the master mode of the airplane. There are three primary master modes - Air-to-Air, Air-to-Ground, and Navigation. The master mode is selected using the A-A and A-G buttons on the ICP - press the button for the mode you want to activate that mode, and press it again to get back to NAV mode.
Each mode has its own HUD and MFD settings. For example, if you select the FCR, TGP, and TGR pages on your left MFD in NAV mode, when you switch to a combat mode after arriving at your destination you will find that those pages are no longer available (the FCC has reverted the MFD back to its default for the A-A mode). However, if you switch back to NAV mode, the MFD configuration you selected will still be there. For this reason, it is important to set up your MFDs in each master mode before arriving at your target.
The master modes have the following effects on your avionics:
Selects the FCR in CRM-RWS mode on the left MFD and the HSD on the right MFD. No weapon is selected.
Selects the FCR in CRM-RWS mode on the left MFD and the SMS page on the right MFD. The first available air-to-air missile is selected, or guns if there are no missiles remaining.
Selects the FCR in ground map mode on the left MFD and the SMS page on the right MFD. The first available air-to-ground weapon is selected, or guns if there are no bombs or missiles remaining.