Welcome welcome! Not that I didn't already say that lol. Anyway, I have a fucking brood here as large as I do at SA.
The biggest differences for the chars I have at both are probably:
Bellamy has never had Echo at SA. And has obviously gone through way different trauma there re: having to go back to Mount Weather previously on a mission and shit.
Lucy is 21 here, rather than 18, and was an early arrival - meaning she's been here longer than the start of game.
Elijah is from the same canon point, but he's with Hayley here - unlike at SA where she's not there.
Margo has PGH history from Atlantis cause I dropped her here for a bit and wanted to give her that when I brought her back to make canon updating her easier. She's also from a different canon point in The Magicians. She's end of S4, rather than end of S3.
Jacen has the same PB here, but Maxi plays Jaina here rather than Lena and she has a different PB.
I think everything else is the same for my cross-over chars? I figured that was a good place to start rofl, even if just so you have a random reference point for differences haha.
Its gonna be weird for Bellamy either way since she's been gone over 6 months at this point and he was always from post-time jump in the show so they were together for him. So I think as far as SHOW canon goes - it depends on how much you want her to trust Clarke and Bellamy? And how much going either way would make that more difficult, more fun, or easier to play? I really am okay with whatever way you go as long as its the best and most fun for you!