I made changes to some of my files in my local repo, and then I did git add -A which I think added too many files to the staging area. How can I delete all the files from the staging area?

After I do that, I'll just manually do git add "filename".

You can unstage files from the index using

git reset HEAD -- path/to/file

Just like git add, you can unstage files recursively by directory and so forth, so to unstage everything at once, run this from the root directory of your repository:

git reset HEAD -- .

Also, for future reference, the output of git status will tell you the commands you need to run to move files from one state to another.