Hey there!

I have the same setup and it works great!

You'll definitely need to put the SSD in the hard drive bay and leave it there. The SSDs I've tried haven't worked very well in the optical bay.

If you'd be using the MackBook Pro to install Windows onto the SSD, you'll need to do that with the optical drive still installed -- on that model MacBook Pro there's no way to install Windows via anything other than the internal optical drive (USB sticks and external optical/hard drives will not work) ...

After you've got your OSes and stuff installed and running on your SSD, then you can swap-out the optical for your old mechanical HD. Be aware, though, that if you have to reinstall Windows, or repair it from a bootable recovery disk, you'll need to get the optical drive back in the machine ...

As for Windows running apps off a second disk, I've never tried that -- I don't know if Windows needs those apps to be on the same partition as the OS or not ...

Other than that, there shouldn't be any issues -- I have three laptops that have run very well with that configuration. And with the possible exception of maxing-out the RAM, installing an SSD is probably the single best improvement you can make to those machines -- you won't believe how zippy they are! =)