The Flex Builder installer does not like Eclipse 3.3. When you try to install it over eclipse, it says the destination folder is not valid.
I found some instructions on how to manually plug the FlexBuilder components in Eclipse 3.3, provided that you installed it as a stand alone application. But it contains a small, but important, error on the directory layout, because the "plugins" and "features" directories must be inside "your-new-extension-point/eclipse". That is, the directory structure inside the extension point should be:
./ /eclipse /eclipse/.eclipseextension /eclipse/plugins /eclipse/features
Other than that, everything went OK following the instruction of the article. The only other different thing I did was to only copy the com.adobe.* plugins and features. But it worked either way.