Thread-dump is always written to stdout and Tomcat redirects stdout to catalina.out by default. You can change where it redirects the stdout to but you can't separate thread-dump from other things written to stdout.
Sounds like you have other debug information written to catalina.out. Maybe you can get around this issue by writing all your debug messages to your own log so catalina.out is reserved for thread-dump and a few other things.
See my answer to this question on how to create your own log files,
How to configure logs/catalina.out of tomcat 6 for per-app. (Configure web-app specific log file for sys.out, sys.err)