Here’s my thoughts from when I ran GoSM:

Ghosts isn’t really a campaign. It’s a really un-connected series of individual mini-dungeon crawls. In particular, if you were hoping for a focus to be on the three factions within Saltmarsh itself, I will warn you that almost none of the modules have anything to do with that. The leadership divisions in Saltmarsh are just kind of there to help DMs build on their own homebrew stuff. Despite much being made of the Sea Princes, they’re more or less unmentioned in the rest of the campaign, as are the other two factions.

Notably, the modules’ antagonists break down into two major categories:

• Underwater creatures (Sahuagin in ‘The Final Enemy’, S’gothgah the Aboleth in ‘The Styes’, and a giant octopus that’s more of an environmental hazard in ‘Salvage Operation’).
• Undead (Isle of the Abbey, Tammeraut’s Fate).
• There’s also some unconnected pirates in Danger at Dunwater and a random priest of Lolth in Salvage Operation. The mini-encounters (Cove Reef, Wreck of the Marshal, Warthalkeel) are kind of just there. You might notice there’s no real theme here. Like I said, this is very open to homebrewing.

In my case, I decided I liked undead as a final antagonist better than an Aboleth. The entire thing became a plot by Orcus - my ultimate BBEG - to drown and slaughter everything in the Saltmarsh region. Everyone else - Syrgaul Tammeraut, the Aboleth S’gothgah, the Sahuagin - were either intentionally or unintentionally working towards Orcus’ goals, some being duped into doing so. This required some reskinning - the generic evil cult in ‘Isle of the Abbey’ and the Lolth priest in ‘Salvage Operation’ became Orcus worshippers.

In your case, if you want to focus on the three factions of Saltmarsh, I think you could go two ways:

• Have reach of the modules be a task or threat created by each faction. For instance, maybe the Loyalists send you on the Salvage Operation, hoping to get some dirt on Anders Solmor’s mysterious missing parents. Maybe the Sea Princes are stirring up the Sahuagin to attack Saltmarsh to break the King’s control, etc.
• Have one BBEG running all three factions. In this case, again, I would encourage you to look to either S’gothgah the Aboleth, or whoever Syrgaul Tammeraut’s magical patron is. Perhaps they are simply playing all three groups against each other to leave Saltmarsh depleted and ruined, at which point they will move in.

In either case, the political side of Saltmarsh is relatively undeveloped, giving you lots of room to work in, but also lots of work to do if that’s what you want.