I'm not sure if this is what you are asking, but this is how we do it.
We namespace all of our projects in a consistent manner, user controls are no different. We also namespace using the project settings window, although you could do it through a combination of the project window and in code.
Each solution gets a namespace like this:
[CompanyName].[SolutionName].[ProjectName]
So, our user controls are normally in a project called "Controls," which would have a namespace of:
OurCompany.ThisSolution.Controls
If we have controls that might span several different solutions, we just namespace it like so:
OurCompany.Common.Controls
Then, in our code we will import the library, or add the project to the solution.
Imports OurCompany
Imports OurCompany.Common
Imports OurCompany.Common.Controls
We also name the folders where the projects live the same as the namespace, down to but not including the company name (all solutions are assumed to be in the company namespace):
\Projects
\Projects\MySolution
\Projects\MySolution\Controls
-- or --
\Projects\
\Projects\Common
\Projects\Common\Assemblies
\Projects\Common\Controls
etc.
Hope that helps...