Messed up Topology (Shading?) due to the usage of the Knife Project Tool Dear Blender Stack Exchange Community,

After trying to model a sword (after a concept art) I did run into some issues after using the Knife Project Tool. I am trying to add some Screws using the Extrude, Subdivide Command and Proportional Editing. However, after applying the Knife Project, weird Shadings started appearing.

I fixed the middle indent by connecting it to the rest of the geometry. The screw holes were done by keeping the produced geometry (Knife Project) selected and applying the transformation once, for all of them. 

Now I did ask myself, whether I'd have to manually connect my screw holes to the rest of the mesh,or whether there is another, smarter way. Because by using this method I lose the accessibility of using efficient and clean loop cuts. I certainly do want to avoid ngons and poles as much as possible.

By the way, never mind my weird Subdivisions in the screw hole, I was going to fix it after solving this Problem.
I have had the same problem with shading after using the knife / knife project tool. Unfortunately, I believe there is no sure-fire way to fix this.  One way that may work is to slightly bevel all the edges.  Another is to set the shading of the faces to flat, and leave the shading of the others at smooth.