If you have to get up in the night and it is unavoidable, like having to take care of a small child, or if you have to go to the bathroom, just do the best you can. Some women notice rocky temperatures when they wake during the night while some women notice little impact. Fertility Friend can usually interpret your fertility chart even when the pattern is a bit ambiguous.
If waking in the night is an issue, take your BBT as close as you can to the same time each morning and choose a time that is likely to be when you have had the most sleep. For example, if your toddler wakes up every morning at 6 am, then take your temperature at that time, even if you go back to sleep. Try to avoid taking your temperature in the middle of the night, even if you seem to often get up at the same time. Pay close attention to your other fertility signs and make sure to record them as well.