I have the stairs prepped, but I noticed that the risers and the treads that are there already are not square. Do i use shims to square up the risers and treads or is there another way? Do I stain the treads and risers before they get installed or do them after?
You need to determine why the risers and threads are not square. The problem might be the stringer. then determine if shimming is the way to go.
If you've got the space and the time, staining the risers and threads before installation might be a whole lot easier than crawling up and down trying to stain them.