Media center is not designed to run on two screens, there are tricks to have it 'release' the mouse so you can use it on the secondary screen, but I prefer to use a 'real' remote to control it.
I know some use a build-in 7" touchscreen that clones the display, the media center is controllable that way because it scales, if you want to use other things (like file-browsing) then yes you might get into problems with scale.
IR remotes including eHome receiver are about 25 euro.
I run the media center on the second screen (connected to a beamer or LCD TV) not in clone mode, I use the primary screen in its native mode for the rest (my current HTPC is a laptop actually).