There are differences based on the tradition. Get to know the details by asking your respective Acharya-s or elders of the house.
I think it is done separately. Even in this traditional differences exist. Each tradition follows different practices. Ask the relevant Acharya-s or elders.
Ashtakshara mantra japam is done during all three periods.
Charama shloka is not recited the same number of times as the Ashtakshara mantram. At least, it must be recited 10 times.