Basically the idea is like this: If a faction is in control of a settlement (via War Always Changes) that is neutral to you, a "representative" or a "commander" will spawn inside of that settlement. (Or, a war planner desk or a flag will spawn if one isn't already there.) Basically, you talk to this commander (or activate this flag or desk) and you can negotiate them to turn it over to you without fighting. This can be done by passing a series of speech checks (requiring very high charisma and perks), paying a lot of caps (I'm talking in the 4000-10000 ish range here, depending on the state of the settlement), or giving the faction a lot of items. Those items that they demand are the same ones that faction uses for recruitment bonuses (IE If the settlement is occupied by the Liberator Brotherhood from the BOS Faction pack and you're playing Liberator Minutemen, they'll demand lots of energy weapons.) Once the negotiations are completed, you will get the option to turn it into an outpost (if you are a conqueror, you enslave all the civies) or a vassal.