So the joining of other factions would be done at the war desk? Once the faction mod is loaded? I see Minuteman and SuperMutants... and Redguard...
You will use the War Desk for any and all Faction Packs*. Be sure to go to this category on the Nexus for current Faction Packs to pick your favorite so far:
https://www.nexusmods.com/fallout4/mods/categories/67/
Be aware that you are leading the faction provided by the Faction Pack, which can be a different faction than the vanilla one even though they may have the same name. My Triggermen Faction Pack makes you the leader of my "designed" Faction, but the regular vanilla Faction of Triggermen will be neutral or hostile to you depending on what's what. Same with Super Mutants. The Minutemen is yours pretty much either way.
Just curious as how the inner workings of Conqueror with Jammer is affected.
Jammer is just his own faction of raiders. You can join him too or ignore him completely. You could probably even shoot him dead (not sure, haven't tried). If you join with Jammer and take over Hangman's Alley, but you are also the Faction Pack leader of Super Mutants and take it for the Super Mutants right after - guess what Jammer does then? Nothing. Not sure there is currently a thing in Conqueror that makes Jammer pull a Preston-Hates-Overboss scene.
I have built the cities and scouted them out just to get a feel for the mod. Are there any settlements on should/shouldn't claim? I have generally tried all settlements as "independants"... except Sanctuary/Red rocket. But I see the trailer or King Gath's video of Jammer setting up in Sanctuary.
Sim Settlements team is working on a few settlement bugs like a dang immortal molerat at Starlight that causes problems, and that should be done very soon. Prebuilding settlements, however . . . better leave those alone when prebuilding that Conqueror suggests you avoid (quests, other troubles).
Once you do the quests there (talk to Codsworth/kill flies, obtain Dogmeat, complete Covenant, become the Mechanist, enter Vault 88, etc) make it an Outpost!
If you save the Museum group, I would guess Sanctuary can't be taken, or do you end up fighting Preston to take over?
You can attack and kill Preston's refugee gang anytime you want. If you save Preston and they build a city at Sanctuary for you, but you then decide to attack it as an Outpost, you will end up killing them. If you decide to make them slaves, however, I don't know if Preston will still give Minutemen quests. I wouldn't count on it.
PS - seems from the civilian comments, I need a fire department and a brothel... not sure how to build those!
I don't think there's a sim plot that is a fire department yet (why?! add-on authors! why?), but there is an add-on by Eldarth that has brothels (regular and interior). You have to manually choose them, however. Also one of the civilians wonders why there isn't a radstorm shelter yet. Add-on authors slacking I think.
* At some point an ambitious Faction Pack author will add their own version of Jammer and have quests, but that is not this day. This day we fight!
