After I installed the Windows CE 6 SDK and SQL Server Compact Edition Server Tools and I don't see a CE 6.0 emulator in the Emulated Device Manager list.
There is a Windows CE 6 SDK entry, but it opens a Windows Explorer browser looking for *.dess and *.decfg files. I found some but they are all files with GUID file names, that I think for the CE5 and Mobile products that I do see.
They may be in Platform Builder for CE 6 but I think that needs to be licensed. I'm not building a platform, just trying to write an app for one.
In order to use the emulator, you need to install a BSP that has emulator support. Unfortunately, the few device BSPs I've seen do not include emulator support.
If you have Platform Builder, you can make a basic OSDesign for your architecture and generate a BSP with emulator support, that's what I had to do.