we also have had different waking times. i managed to chart fairly well regardless, all i would do was just head back into bed and try to get my body back to resting (ie heart-rate back down...even a wee little nanna nap lol while DH took DD and got her breakfast). as long as when you enter the time correctly in FF (or whatever program you are using) it can be taken into account. i always aimed to get my temp in sometime around 7.30am and 8am (DD would usually wake at say, 6.30-7am). it's of course not ideal, but it still worked for me in the sense that it did still have my own pattern of temps that i could use (and FF could use) to help indicate ovulation.

HTH!