The overall answer is - just do it whatever way you think is best, there's no objectively correct way to do it.
Personally though, I list everything I watch and read, including sequels and spin-offs and everything. I also give every separate entry its own score, so sometimes season 1 and season 2 might get different scores from me for example. The only downside with listing everything is that the "Total anime" number on the stats page is a bit more inaccurate, since a big part of it is sequels and stuff. But I don't care much about the stats anyway.
