Our product is an ASP.Net web application. Currently, we use Web Site Projects in Visual Studio, but have been looking into using Web Application Projects for quite some time.
By using assembly WebResource you can Add CSS/JS/Some other File as Reference along with the Code i.e, your Base Project DLL.
If am right you can Add this WebResource in your base project then go through the below link.
http://support.microsoft.com/kb/910442
Like this way, most of the third party tools will access their CSS and JS files.
Try this. Hope it will help.