The reason there is a custom.css is for you to add your own css which will overwrite the default css that is within any theme
Then whenever IPS release upgrades then everything will get upgraded and leave your css in the custom.css alone
If you make changes to any other css file or any template then those files WILL NOT get upgraded without you 'reverting' back to original then re-adding your changes
Soas you can see makes life a lot easier in the long run.
You can add further css files if you wish but that would be another tutorial at later date