I'm not familiar with AlivePDF specifically, but it looks like the ZIP files provided on their download page are Flash Builder projects of a sort. You can expand the ZIP file and then import the project through File | Import... | Existing Projects into Workspace
The project organization is a little different from the current project format, though; you should probably direct questions to the AlivePDF forum at http://alivepdf.bytearray.org/?page_id=12 .
-- Tom Kraikit
Flex SDK engineer