Welcome to the forum Daniel. The way your question is worded, I can not tell if you are asking a general question about how Windows automatic default save locations work OR you are asking a general question about how a user should organize his files when using manual "save as" actions. I don't want to overwhelm you with specifics until more information is provided about exactly what your objective is. Getting into everything involving file types, why windows saves them where it does, and default folders is a hairy place and I could easily lead you in the wrong direction.
Is your question just a general one, or are do you want to specifically change where your files are stored by default?
Please state in more detail what it is you want to do. Screenshots are helpful.