To clarify, we applied while in USA (you MUST be there when submitting application and can only leave after biometrics are done (or you get a receipt notice saying you don't need them if they were done recently enough). So definitely don't go anywhere until you apply! (Otherwise you'll need to come back). And I recommend having an immigration attorney fill out the paperwork since the risk of a mistake could cause problems later on.

More info: The 6-month thing is only used for naturalization; if she's out of USA for longer than that it can reset the 5-year clock. And 1 year thing (without reentry permit) means she'd need to come in on a returning resident visa (which technically can be granted upon arrival). If you don't have one already, any immigration attorney would be able to clarify these details. Much easier for your situation as you're a US citizen!