If you already have files in ' mywebsite':
cd /Users/me/Documens/sites/mywebsite
git init .
then do a git statusto see what needs to be added.
git add .
git status # check what has been added
git commit -m "first commit"
If you do not already have a file, you can:
cd /Users/me/Documens/sites/
git init mywebsite
cd mywebsite