First some context; we are developing a large desktop WPF application in .NET 4.5 targeting 64 bit Windows 7 and 8. We are using Visual Studio 2012.2 (soon to be .3 then
What I did was make one Solution and made a CUIT project within, I then made multiple Coded UI test's within that. This is good because using an orderedTest you can run them together and they also share a UIMap which helps too.
I also have/had this problem, because we are at the beginning of using CUIT. For now the CUIT remains in product solution. We do this because the tests should remain in memory of developers. When tests stay in on solution I'm afraid they get lost in oblivion. But indeed there is sometimes a bad feeling that the CUIT pollute the products solution, so i guess they will get their own solution after some time pass and the test become established.
Edit: If you use different Versions of Visual Studio you have to consider that for example a VS Prof. can’t build a solution with Code UI Tests. This means in “multi VS-version environments” you have to separate Coded UI Tests from “real” code.