I'm awake at 9 a.m , bed again 1 -2 a.m , what's the best times to take my 2 x 25mg topiramate ?

Time for Meds: I suggest you take your medicines about 930-1030 both times. You want to space them out to twice per day. The timing does not need to be exactly 12 hours, but something close to that would suffice. People who use this medicine for headaches sometimes take it just once per day. Normally at bedtime.

Depends: If it makes you sleepy take it soon after rising and just an hour or so before going to sleep. This medication can have paradoxical energizing vs. sedating effects depending upon the person. 25mg is a pretty low dose so you will likely find that whatever side-effects you may have will dissipate rather quickly. That said you don't need to take it exactly 12 hrs apart 8-12 hrs should be sufficient