After fiddling with Sharepoint WSS for most of this week, getting advice from some Sharepoint geeks, reading the documentation,googling a lot and hanging out in the newsgroups, I have finally worked out that what I want to do is use a combination of all of the methods of working with WSS.
My plan at this point (and don't hold me to it) is to use the default site for the administrators. They can figure out how to get around the tangled mess of using multiple layers of workspaces to control permissions and access. Then for the two separate user access sites (one project requires file collaboration and the other, for a totally different audience, will just be to share read-only files), I will write ASP.NET applications using a combination of the Sharepoint API object model, Sharepoint Web Services and hand rolled code that will directly query the database. I will probably avoid web part pages and web parts since I am just building my own site, though there is gobs of great info out there on how to build them.
It was a lot of work to come to this, but I'd call it ultimate flexibility!!