The portal is intended for navigation, organization, aggregation..., NOT for collaboration and content. WSS is where the work is done. Just because you can create lists at the portal level doesn’t mean you should. It’s a good idea to be careful to maintain this distinction. It will save a lot of headaches in the long run. That’s my two cents, I speak from experience…
Oh, and I would be very careful about any customization of the portal. It’s a bit different than WSS, and it seems that it was not intended to be customized extensively without a lot of work.