I check it when my app is in actual game play mode. If it is in some sort of message or menu display, the app handles itself well enough because there aren't any physics things going on.
I call my handleReturnFromBackground() if GetResumed() returns 1 when checked in my main processing loop.
What I do in my 'handleReturnFromBackground()' function is to reset the allowed orientation, set the desired orientation (this is a command that is available in Tier 2 only), reset my Physics Gravity and sync rate. Then, if actually playing, it puts the game in paused mode.
Pretty much any of the steps you do to set up the display and environment (aside from loading files and creating sprites) probably should be done when you detect a return from the background. Just to make sure that everything is set the way you expect it to be.
Cheers,
Ancient Lady
AGK Community Tester and AppGameKit Master