Chapter Three is in love with Panels. A lot of people are, and with good reason. It has the power to eliminate the need for theme developers, especially with the development of Panels Everywhere.
I have recently returned to Drupal after a long hiatus and while a lot remains familiar, Panels is one of those modules that has grown into a wild, hairy beast. I can't really tell you what variants or contexts are used for, and I'm not quite sure why I have to save twice when updating anything on a panel page. There is scarce documentation about using plugins, and I wouldn't necessarily describe creating a plugin as "fun". But it's a learning process, eh?
So I'll share with you some of the best practices or problems I've encountered, and then maybe Merlin of Chaos will magically appear and comment that there is a far simpler way of doing it. Or maybe some of you have different approaches that you'd like to share or can find faults with my approach?
**EDIT** I highly recommend reading all the comments attached to this post, Merlin of Chaos did appear and explained a few things, particularly how to specify an alternate admin theme and css without doing my hack.
In this blog post I'll discuss how to make your theme aware of panels, as well as how to create a custom panel layout plugin. Read the full post here.