As all Windows applications do, iFly responds to the Alt-spacebar combination.
To minimize the app to the taskbar (and keep it running), do: Alt-spacebar, followed by N (or click on Minimize). At that point the app now just shows on your taskbar and you can see your Windows desktop & taskbar again. BTW: even in its default mode of taking over the whole screen, the taskbar is always available to you by hitting the Windows key (between Ctrl and Alt) on your keyboard. That way you can quickly switch to another app you have running (with iFly filling up the rest of the screen in the background).
To resize it so it shows, but doesn't take up the whole screen, do: Alt-spacebar, followed by S (or click on Size). At that point the cursor turns into a four-arrow and you can "grab" the edge of the app window and drag it in or down to make it less than full size. That being said, I just tried it again, and I'm having trouble making grabbing an edge. Anyway, it did work for me, and currently iFly is in the lower quadrant of my desktop. Unlike other Windows apps though, since there's no title bar to grab, you cannot reposition the app to wherever you want on your desktop. Once you have made the app smaller, you can go fullscreen again by doing Alt-spacebar, followed by X (or click on Maximize). [Note: it seems that I always have to do the Maximize twice to get it to work. Weird.] To then reshrink it, do Alt-spacebar, followed by R (or click on Restore).
A note about resizing the app though: it messes up the sub-windows, like Menu or Flight Plan -- once you've resized iFly itself, even if you go back to fullscreen, you can't see all of the sub-windows and so won't be able to do some things, like, I don't know, gracefully exit the app.
Anyhoo, just thought someone might find one of these tips handy. Mainly the one that sends iFly to the taskbar so you can keep it running but still use the rest of Windows normally.