What are you trying to use FC to create? a website or app?
If its a website then you just use the swf and the folders that FC builds when you export.
If its an application then you can have FC build it for AIR.
Or maybe you are looking to use it for more than its intentive purpose? Maybe the Flash Professional is the program you and your company is looking for.
Catalyst publishes to a swf file. You can convert that swf file to a standalone .exe or .app file using a Flash Projector. See this discussion for more details:
You can create links using the "go to url" interaction in Catalyst.
You may find the Catalyst Examples thread helpful in terms of getting a feeling for what Catalyst can and can't do.