There are quite a few related posts further down this forum about the time VS2005 was beta. Re: the emulator it's native code now so you don't need to build differently as such.
Looks like you have linked in the wrong PocketHAl if you are seeing the wrong version in your app.
It took me about 2 weeks to understand VS2005 enough to build/deploy/debug happily so take your time & it will come right.