The reason for the faces being below the surface is that the vertices and edges that make up the faces in those regions are not on the highest points of your mesh. When the faces are made, they connect in a straight line, which in this case goes through a portion of your mesh. The two ways to deal with this are to add more vertices so that the faces can follow the contour of your mesh better, or reposition your vertices so that the detail is better preserved. If your end goal is baking normals, you will want both objects to be as close as possible. Here are a few tips to make your retopology process a bit easier:
1) Instead of starting at one point and working your way around the ear, start by identifying where you want your edge loops to be, and what details you want to highlight.
2) To do this, I've always found it easiest to use snapping set to face, and then Ctrl click to extrude a single vertex and create your edge loops. If you enable automatic snapping (the little magnet icon) each new vertex will snap to the surface where you click.
3) Place your edge loops at the highest and lowest points possible. If there is a ridge or bump, place the loop so it is on the highest point. Do the same for any valleys or indents.
4) Keep in mind that you will have to connect all of these loops together eventually, so plan where each vertex will connect to the others.
5) Finally, begin connecting your edge loops to each other. You won't have enough edge loops to simply fill single faces between edges, so add more vertices where necessary. If you use some topology guides and plan your topology carefully, it shouldn't be to difficult to add in extra detail where you need it.