You have a couple of options. You can simply take your temperatures after 3 hours of consecutive sleep each day - no matter when that happens. You should still be able to see the overall pattern.
If not, you also have the option of learning to chart using mucus-only system. The Creighton Model and the Billings Ovulation Method are both mucus-only methods of charting, and go into much more specific detail in terms of understanding your mucus patterns - so that you don't require any additional data (temps, cervix, etc.).
The Billings Ovulation Method
www.woomb.org
The Creighton Model
www.fertilitycare.org