Trouble with ASP.NET trust levels on IIS 6.0

I just upgraded my Win2k Server machine to Windows 2003 Server and IIS 6. Everything worked fine. I then installed Windows Sharepoint Services and now none of my apps will run, some throw an ASP.NET error that says "Debugging is not supported under current trust level settings" and some can't be found by the browser at all. Any ideas on what could be going on? After the upgrade IIS was running in IIS 5 Isolation mode, but Sharepoint Services made me uncheck that. Now I can't get anything to work except sharepoint and I am getting frustrated. Any ideas? Thanks!

-JoshWindows Sharepoint Services and regular ASP.NET cannot coexist on the same web site. They can be on the same server, but you have to have separate sites for them. Two different virtual directories won't do, they actually have to be on different sites.

The reason you get this specific error is that WSS switches its site to a reduced trust level for ASP.NET. At this level, debugging is not supported.

There are other things WSS does as well, which won't play well with your site. WSS removes a lot of the modules typically used in an ASP.NET app, like session state, and also installs a filter that may rewrite your site's URLs (because, in WSS, most pages actually come from the database rather than from the filesystem).
Thank you so much for you answer! It was driving me crazy, because each time I uninstalled/re-installed WSS my website would work/stop working. I wonder if that is in the readme? Very good to know!
Thank you so much as well! I had the same problem!

The trouble is, the code I am going to develop I want to use it on the sharepoint site (via web part)... this limitation just makes the development more difficult.