To sync the mods with the ones that are written in the manifest.json, run the syncmods.bat (Windows) or syncmods.sh (Linux/MacOS) script.
To copy the overrides you changed to the pax/modpack/overrides folder, run the sync_overrides.bat (Windows) or sync_overrides.sh (Linux/MacOS) script.
Notice: Everything else than mods and resource packs is an override. (For example configs, scripts, resources.)
Use pax using cmd or terminal. To see how PAX works it's recommended to go check out its wiki: here
To tocate the pax folder on your computer, use ./cd to do that.
Windows:
$ cd .\minecraft\pax
Linux:
$ cd ./minecraft/pax