In the Seafarers expansion, you build ships adjacent to each other, thus forming shipping routes along the sea hexes and connecting the islands. If your shipping route has reached a new island, you may build a settlement there. With two exceptions, in Seafarers the rules for ship building are the same as for road building. The first exception is that roads may not be built on sea routes and ships may not be built on paths. The second exception is that open ships may be moved.
While in Seafarers the ships are strung together in a static fashion, in the Explorers & Pirates expansion the ships can cross the seas like real-world ships. If your ship carrying a settler reaches a new island, you may build a settlement there.
In these two expansions, the ways of using ships and settling new islands are so fundamentally different from each other that it is impossible to combine the expansions. Besides, combining them doesn't make much sense anyway. If you use a settler ship, you reach a new building site for a settlement faster and more cost-effectively than when stringing together various ships.