I was re-watching some videos of container city and I got to wondering; when playing with friends, will the commander and those troops he has following him escorting the drone be replaced by your friends with jump in jump out co-op or will they just live indefinitely? And if they will be replaced with your friends will they be in the cut scenes with custom character models?

I was a bit confused about that aspect. Thanks in advance.

Every player who is in the lobby will take a spot of those NPCs.

We are not sure wether player characters are actually part of the main plot (speaking characters), or not.
Personally, I think they are in Campaign mode.

I hope it will be like how your multiplayer character is the same as your campaign character in Halo Reach. You are your customized character in both gameplay and cutscenes. That was a big plus in my book for Reach's campaign, and hopefully Brink is the same way.

Yeah, that's the way I imagine it as well.

If a player starts playing the campaign (wether it be offline, coop or online), his character will take the main role (which, iirc, is one of the two brothers). Every other player who joins "his" game will take the position of the other characters then.