The secondary drain is in the soffet so that you can see there is a problem, if the primary drain backs up.
Sounds like the 2in drain is getting plugged up and overflowing. Is the 2in pipe trapped? If it is, sure seal it up and extend a vent higher than the pan, from the top of the 2in opening.
Just remember that the trap will dry out during heating season, and allow sewer gas to be drawn into the airhandler. There are automatic fills for traps, look into them before you commit to sealing it up.
Might just be easier to run a new 1in drain to a more logical location, and seal up the 2in drain.
Last edited by 8 Ball; 08-14-2008 at 07:39 PM.