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.