Couple of things:

I tried using keyclone with EVE a while back and had similar problems with the splash screen and resizing of windows making the mouse offset wrong.

It looks like EVE uses the absolute postion of the mouse so that if you resize the window it's no longer accurate.

You can position windows with scripts - I used AutoIT which is very simple to program - the window name is simply EVE if I recall correctly but you have to wait for the main screen to load before you can work with it

According to the EVE GMs any kind of keyboard/mouse broadcasting is not allowed (there was a thread somewhere about MMOs and their multiboxing stance). EVE doesn't mind you multiboxing but you have to do it the hard way.

I'd suggest grabbing an extra screen if you can, thats what I'm going to do. The other alternative is to hardware multibox and use something like Input Director or Synergy.