First off sorry that I havent been to the site in a bit. Its been tough with school and working on other sites.
For the most part mods can be installed as they normally would. PayBas has not really done any changes to the actual script. Usually you will find that if what your searching for is missing (due to the modx install) then you can refer to the modx install directions and find the line that you edited or replaced and go from there. Being that it wasn't too many files that just makes it all that much easier. The only mods that I have found issues with are the portals. Thats only because they are not working with the shared themes so it seems. Nothing a few quick quarks will fix.
Hope that helps.