The most common method is to look for indirect clues. My wife can usually tell by her sore/cramped muscles (especially the calf muscles), or if she bit her cheek or tongue. Waking up with a headache or disoriented (more so than normal) can also give her a clue.

The more I read on these various epilepsy forums, the more I wonder about whether the majority of folks who have nocturnal seizures also have sleep apnea (which causes a drop in blood oxygen). If you suspect you are having nocturnal seizures, you might ask your doc about getting tested for it.