How to best deal with deploying a solution to IIS as a virtual directory - dealing with relative paths, bin folders, etc...

Question

So we have our main parent portal and our own site under that:

Portal/MySite.

MySite is a virtual directory under the Portal.

The problem is that MySite needs its own master pages, files in the bin folder, etc...

However, the only way to get MySite to work was to move the MySite.dll into the Portal's bin folder.

The problem with this is that references to master pages all have to be updated to: "~/MySite/MasterPages/Site.Master" instead of "~/MasterPages/Site.Master"

Is there some better way to handle this?

To allow me to deploy a separate VS 08 ASP.NET solution to IIS that can inherit things like form auth, session state, etc... but still be able to have its own independent bin, master pages, etc???

Basically I'm asking for a link to a best practices guide or advice as to a better way to do this.

Thank you!