git branches are completely independent of each other. As long as you do a make clean to get rid of old code artifacts before compiling the new code, you can have multiple branches under the same repository.
Your workflow should be something like:
1 git clone the initial repository
2 git remote add any other repositories you want to track
3 git checkout the branch you want to work on
4 make your changes
5 make clean and recompile to test your changes
6 git add and git commit to commit your changes
7 git push to share them with the world
You should only need to do step 1 once. You need to do step 2 for each repository you want to track, step 3 every time you want to work on a different branch, and steps 4-7 as often as necessary.
