Troubleshooting Merge Conditional

I'm having trouble with Merge Conditional. I set a number register where some publications in a style library are "1" and some are "2", and then write the merge conditional for one of them. It's not working, I can't get the publications to do different things.
What can I do to troubleshoot a merge conditional? I checked to be sure the number I chose for the register was not already in use. What else should I look at?