I just delivered an internal MOSS IW Ramp course in Münich and we have some discussions concerning the onet.xml and how to modify the content of the sites, which have been created using custom code directly after site has been created. You are most likely aware that during site provisioning, there's no such event available as the WebCreated, which would be raised when the web creation based on onet.xml has been done. This is quite a huge limitation, but then again, there are quite good workarounds for this.
Step-by-Step guide for manual creating of WebCreated event are the following:
//look for the default page so we can mess with the web partsSPFile thePage = curWeb.RootFolder.Files["default.aspx"];
//get the web part manager SPLimitedWebPartManager theMan = thePage.GetLimitedWebPartManager(System.Web.UI.WebControls.WebParts.PersonalizationScope.Shared);
This was extremely quick sample, but hopefully it's useful to you. I'll try to find some time to make more comprehensive example of this.