From now on, once you enable Offline Gmail from the Labs tab under Settings, you can choose which messages get downloaded. On the Offline tab under Settings, you'll see your current settings and be able to set how much mail you want to download from each of your labels. I chose to download everything in my Inbox and important labels, as well as recent messages from the last month from other labels.
When you hit save, Gmail will synchronize new messages you didn't have downloaded before and remove the ones you're not planning to read from your hard drive. You can always change your settings back to keep fewer or more messages later on -- fewer messages means Offline Gmail runs faster. Questions or comments? Let us know!