Refer to this for JIRA 5.2 - for color scheme:
(Keyboard shortcut: g + g + start typing look and feel - or Administration > System > User Interface > Look and Feel)
JIRA 6 that is coming out soon is cool - since it willl auto-magically match your scheme to your uploaded corp logo (yet you can override it)
For layout - perhaps you are talking about the dashboard or screens?
There's alot more under those covers - but to get you going.
Hope this helps -
Here's some tips I think.
Note the caveats by Penny there.
Also these release notes indicate changes to JIRA CSS styles with 6.0 ("changes to core JIRA CSS styles").
Hmm, I can't see to view https://answers.atlassian.com/questions/160863/jira-customize-css: I get the following message:
404 Not Found
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