You can change salaries by editing the players.dbf file with DB Commander. Note that this can cause problems when you're editing a Dynasty game, so be sure you make a backup first (indeed, make a backup whenever you're editing the databases) and when you're done editing, make sure the Dynasty is still functional by loading it and simming through to the next season (if all is fine, re-load it and continue as normal).
If you're just editing a saved roster then there shouldn't be any problems, though again you should always keep a backup handy just in case.