So I just began the Brotherhood of Steel quest line, and I got onto that quest where you have to search for the missing recon team. At the very end, I killed that old guy hiding in the bunker because I wanted his combat armour, then I lied to Danse and said he attacked me out of craziness. Is this gonna come back on me now? Also have I made the right choice in choosing BOS, how does it work with settlements since mine are currently owned by the Minutemen?
I let Brandis live, and re-recruited him into the Brotherhood.
There wasn't much to do with him after that. He stood around in the Prydwen, moaning about recruits these days, and said he wasn't released for active duty yet.
Only real thing that happened with him, was in the final battle, he joins the group of BoS soldiers who help you.
But he doesn't say anything special during that. He very nearly died on mine after taking a missile to the face.
In regards to settlements, the BoS don't actually get involved.
All your settlements can still be recruited by the Minutemen.
As far as I am aware, the only distinction is that you can now build Brotherhood Flags under the Decoration tab.
I'm not sure that you can. I've read some people saying placing it through the settlement menu (vs from the inventory) may help, and others saying it doesn't.
Via the settlement menu doesn't help much, as it automatically tries to snap the items to certain places on shelves.
And often it snaps either on top of the very top shelf, or in the middle of a shelf.
So it's not very useful for decorating, in my opinion.