Caveat: I'm not part of the SS2 team, but am drawing from my experience playing and from things Kinggath has stated on his streams.
SS2 is basically designed to be played alongside of/in parallel with the main FO4 questline. They've specifcally built "pauses" at various points in the SS2 storyline where one quest ends and the next one doesn't start for a few in-game days. The idea is that you'll more-or-less bounce back and forth between main storyline and SS2 storyline, for example: futz with your settlements, track down Shaun, help Jake with something, check out Diamond City, check back in on your settlements, free Nick, work with Jake again, work on settlements, track down Kellogg, etc. Progressing the SS2 storyline will give you more resources and ability to carry out the FO4 main storyline, and carrying out the main storyline (and working with factions) will feed into and enhance the SS2 storyline (mainly in the way of new recruitable settlers and allies for the climactic battles). You don't really want to grind one then the other.