From WhiterValkyrie in the Xbox guide:
There are four factions in Deadfire and, if you so wish, you can do quests for all of them throughout most of the game. Yet at the very end, before your final voyage, you will have to chose – doing the last quest for any faction will make you unable to finish the other ones. So, if you would like to get all of the achievements listed in this section in one playthrough, make a branching save when you get all the faction quests to this last step. Each faction has their own category in the journal and as such their quests are easily identified.
Royal Deadfire Company quests are given by Hazanui Karū and Atsura (both located in the Imperial Command). Just follow the questline – it is all rather straightforward. The “point of no return” here is obvious as both Hazanui Karū and your journal will point it out. It comes with a quest “The Final Maneuver” – if you do that one, you will forfeit every other alliance and bind yourself to RDC. So, save before agreeing to commit to Hazanui Karū if you want to pursue other faction quests first.
If you have trouble with one quest:
https://pillarsofeternity.gamepedia.com/Pillars_of_Eternity_...