Theoretically, best practise would be not using extra.css (to avoid the use of !important and avoid plethora's of unnecessary style rules that just get overwritten by extra.css and serve no purpose). The only actual (really very mild) performance problem I can see is the unnecessary style rules though.I hope this isn't too nutty of a question but, does it cause anything to slow down at all when the browser has to interpret css and then reinterpret it? (Or whatever happens here?) In other words, should I be using this in moderation or can I sling whatever I want in there?
In practice, using extra.css is far easier, doubly so during beta phase, and allows for disgustingly easy style upgrades.
Bottom line: save your sanity, smack everything into extra.css. I wouldn't worry about performance loss too much, as it will largely be unnoticeable. Oh yeah, and consider minifying it.