Jago
You're thinking in terms of UE2 technology. I think that's the core issue here.
Unreal has changed in UE3. You really should build like you build in Quake. The world is empty - and you add to it. We generally end up with very little BSP remaining at the end of a maps development. Load up any UT3 map and turn off the static meshes (in the game, type "show staticmeshes"). What you see remaining is the minimal BSP.
Try to get comfortable with creating levels using a Quake mentality of adding everything. It makes meshing the level later WAY easier because all you have to do is convert your brushes to blocking volumes.
That's basically what the guy in the topic did:
http://www.3dbuzz.com/vbforum/forumdisplay.php?f=305
He build the BSP shell and then used that BSP as a basis for placing meshes.