I've got a Web Setup Project in VS2008 that is taking the files for two web applications and turning them into a single setup package. This works and I have got it asking for the user to select the application pool but the application pool is only being applied to the project sat in the Web Application Folder and not the one in the Web Custom Folder that I added for the second project. How do I force it to set both applications to the same app pool? Thanks in advance for any help on this it seems like it should be simple but I've been mucking round with it for ages to no avail.