Is SEO affected by sub domain pointers?

hello all,

Kinda new to the forums so bear with me. When I normally install WordPress I have either a redirect or a pointer with the new host I’m using. For example my domain is http://chungkingstudios.com but the folder for my site exists in http://chungkingstudios.com/chungking. Will this negatively affect my SEO ranking? Also what is the proper way to unpack a wordpress Folder into a public_html directory? I’m sure people have different methods so feel free to share yours! Thanks a lot.

-Craig