Hi @Kurt_Frary,
Your master branch is supposed to be your “actual” project. When you are happy with the results in your branches and want to integrate the features you created in those branches in your “actual” project, you could merge the branch(es) into the master branch. See here.
If in doubt, make a backup of your project folder including the .git folder by duplicating it. Save the duplicated folder somewhere else, maybe on an USB stick. To save some free space, you could delete the Library and Temp folders in the backup folder. Do not work with that backup.
Then try to merge your branches in your actual project. If something goes wrong, you could simply replace the broken project with a copy of the backup project.
Did this help? 
See also:
- Forum User Guides : How to mark a topic as solved