generally speaking this is not something that many people do so there's no support for it. There are of course several options:
1) for extensions specific, you can add an a directory in the overrides/ folder in the missioncontrol template directory. In here you can add an override css file. See the other overrides for naming/samples.
2) If you want something 'system' wide, the most 'joomla' way is to create a very simple system plugin, that all it does is add your custom stylesheet to the document object. plenty of examples on how to do this. you could even make it so that your plugin took the custom css from a parameter to allow you to modify it on the fly.
3) you could add it directly to the template's index.php but you will have to be prepared to re-add it after an udpate (not a really advisable solution)