This is not anything new... many people have posted on this very topic. It just took me awhile to find the links so I'd like to put everything in one place that is easy to find.
1. Download the latest SDK (currently 3.2).
2. Create a new folder called "3.2" in the following directory: Program Files/Adobe/Flex Builder 3 Plug-in/sdks/
(Replace Flex Builder 3 Plug-in with whatever your Flex3 Folder is called)
3. Unzip the contents of the SDK zip file to this folder.
4. Have the SDK Target Flash Player 10 by following these instructions.
5. In Eclipse, go to Windows and open up the Preferences. Off to the left, click on "Flex" and then click on "Installed Flex SDKs". Now on your right, click "Add" and browse for the 3.2 folder you created in step 2.
6. Now you should have Flex 3.2 listed as an available SDK. Check Flex 3.2 and click Apply.