In most of the cases you reuse the high poly mesh to build the low poly, simplifying the edge flow and collapsing what is not necessary for the details or silhouette of the object. In hard surface straight lines must be straight, flat surface flat, cylindrical shapes must have the correct curvature, etc. You can use the same techniques used in organic retopology, but you have to precisely snap the mesh to the high poly surface, methodically following the contours.
You probably need to follow more tutorials, there are many on YouTube.
The mesh, internally, is triangulated even if you don’t see the triangles directly, and the game engine you are going to use, will triangulate the mesh when importing. The triangulation will happen with a “random” orientation, so, the normal map you baked with an edge oriented in a way, will not match, creating shading issues.
You have to use quadrilateral polygon as much as you can, and, before baking but after UVing, triangulate the whole mesh.
In regards to your original post–bake the hole onto a map. Don’t have actual geometry represent it in the low poly. There’s just no need. Only match the geometry when needed like in a gun barrel (see below.)