What we recommend is to set up at least two branches. Master should correspond to the upstream master branch, you can pull changes from the official PX4 repository into this branch. Your own work should be kept in a development branch, consider this your own main branch. From this development branch, you can branch off again to develop different features, and merge them back into the development branch when they are finished. At the same time, you can also pull in changes from master if desired. This is summarized in the graph below.