Molly, I had the same problem when I started using keyclone and thought I was going mad too

What you want to do is go into keyclone options, click the do-not-pass button and then set each of the keys you use for movement (eg WASD) in the box there. When you do that any time you press one of those keys on your main it wont be passed to any other instances of WoW.

You may also want to use the override key if you use any of the letters you dont pass in your password, if you have all accouns set up with the same password and just type it once to log on all instances at the same time.