Are you having trouble with any certain spell or ability referenced in the mods you linked?
Generally speaking, if you install one of those mods in your override folder, they will supersede any of BioWare's patches. The only caveat there would be script-related, but I don't know of many (if any) exceptions.
For the most part regarding ability mods, you can generally use whichever mods you like and disregard BioWare's patches when doing so.