I don’t think nested repositories will work as expected, as by default git will include anything in the main folder as part of its repository – excluding ./.git – so changing branches in the nested repositories will likely have unexpected consequences.
Then you can delete the .git folder in each sub-repository to have a single big repository. Although, depending on what projects you have inside and how you handle them, it may not advisable: grouping projects “living” together makes sense, grouping unrelated projects less so.