Since we do not have an upload control functionality yet you would have to manually add the user controls to the folder structure of your websites.
If your DAL and BAL projects are common across all of your Sitefinity projects you do not have to include all Sitefinity projects in the same assembly. What you can do is to create a folder called Reference Assemblies where your projects will dump the latest version of their dlls. Then your Sitefinity projects will have references to your dlls located in the Reference Assemblies folder.
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