Hi Mate,

welcome to the wonderful world of multiboxing. When you run keyclone it will pick up all running sessions of wow, which is the idea so what you need to do is go to the command page in keyclone and set your maxfps (max for for the foreground) of your main toon command to whatever you want - say 60, then set the maxfpsbk (background fps) to something like 15 and repeat for the alt.
The effect is that when the main screen has focus the alt screen will run at a max fps of 15 and the main will run at 60.

Just realised you're probably not using keyclone to start all wow session, you should so you can make these settings and make use of maximiser. Go to the keyclone webby as it has a really good faq and walkthrough on how to set it all up.

http://solidice.com/keyclone/index.html

Hope this helps.