Just delete the faces of the wing that are inside of the fuselage, then Combine the two polygons and merge the verticies. Your going to want to use the Split Polygon tool again so you have "mates" for each vertice of the wing. Currently you have many many more divisions on the wing than on the fuselage it is going to attach to, so do a bunch of split polygons around the fuselage that match up with the wing verticies.

To add detail in Sub-D mode, when you get to it, all you do is switch to Vertice mode as you do with polygons and move them around to make the shapes you want. To add more detail you need more verticies, which means you will need to use the Split Polygon tool (you can use it in Sub-D mode too) to split the areas that need more divisions (and thus more verticies to move).