Well I've come up with a solution that works for me.
The secret is another application called PCKeyboardHack from here...
http://pqrs.org/macosx/keyremap4macbook/extra.htmlThis allows you to remap the Ctrl-R key to the command key. Simple as a tick box.
As the keyboard on my Macbook Pro doesn't have a Ctrl-R key (only one on the left) I can safely remap it without the need for multiple keyboard profiles.
I found this from the link that theferenc gave out. Seems to be an essential add on to get the magic from the main application.
It's also allowed me to remap my caps lock to a keyboard shortcut. In my case Option-Space, which fires up Alfred (similar to Quicksilver or Launchbar).
Now thats really good as I've always thought caps lock was a waste of a perfectly good key.
I couldn't get Spark to work due to the security policy on OSX.
Ukelele does look to give the complete control of the keyboard but I'd already got to a solution that works for me before starting to play.
Over the next couple of days I'll have a play and see if it can get it up and running.