I figured it out (pretty easy). Since sedebug outputs straight to the command window anyway I can just use the diary command.
>>diary on
>>sedebug('model_name')
sedebug>>cont
If anyone knows a quicker way or a way to do it through the debugger directly while suppressing the output let me know. The reason I ask is because the diary output is about 240 MB so it's a little slow to use.