Can I assume that your ASP.NET pages are in an unmanaged path or possibly in a separate virtual directory?
[slight change of topic here]
What I would really like to do is have two separate WSS sites on one server, along with a standard ASP.NET web site. This would allow me to jump out to standard web pages when I need to do some high-end, out of the box feature, while supporting two organizations with the WSS sites. Each site would have its own template/CSS for banners and page decoration. Of course, just to make things interesting, my boss wants Project Server to be loaded as well. So ideally I am looking at a structure like the following:
<root> ASP.NET site
|
|- default.aspx
|
|- <\Org 1 - top page WSS>
|
|- <\Org 2 - top page WSS>
|
|- <\projectserver>
Is this feasible to do? Can I embed separate virtual directories under a standard site, or do they need to be in a peer relationship? I haven't experimented with virtual servers/directories enough to know which way to go.