Are you saying you have a "Web Site Project" that started out as a "Web
Application Project"?  -- because from your post, it is unclear.
Peter

You have what's called a mess. Ultimately you will want to build your project
and deploy your project, because you will not copy the project.
Now if the project started off  as a web application project (using the vs
2k5 plugin) it should remain that way.

Personally, i do not prefer this method - only because it requires you
rebuild the whole project every single time a change is made which slows down
development, however it does make deployment easier because it eliminates the
randomly named assembly file names.

Hope this helps.
What ever your team decides to do you should do it as a team and the end
goal should be to get the project to compile properly so that you can publish
and deploy the site properly without any unseen surprises down the line.