I have a section on the mesh I want to make circles on, so I'm trying to make clean topology on the mesh, I tried a few methods, and only one seems to be clean (Blue rectangle selection) when I add the sub modifier and Red MatCap. So what would be the best way to add the circles in that particular selection, without adding the shrinkwrap modifier, or is this the only solution to avoid bad shading?
I don't say it is the best method, but it is a method without the shrinkwrap modifier...
Select some vertices...
F3 -> search for looptools -> Circle
and you get
choose individual origins
select ring vertices again
E -> S -> move mouse a bit
E -> Z -> move your mouse....
ok...for a better result, you should subdivide after select ring circle and then looptools -> circle again...
then you get: