Don't they send you to find the faith lapis after the desert? You wanna head to Aquillak town. Follow the in game hints.

Admittedly I didn't find the entrances to DA B, or D with the boat. Those bosses were a breeze by the time I got to them. I'll have to do a more thorough search on my next run through. Thank you for the info.

Feels somewhat stupid of me to have to resort to asking, I can't seem to be able to find my way into danger zones; B, C, and D. Any pointers would be appreciated, thanks.

Edit: found my own answer. For anybody else stuck on this, without spoilers, just continue the story line.