Instead of the "big" 2x3 pin header, check these out:
http://www.newark.com/mill-max/0922-0-15-20-75-14-11-0/spring-loaded-contact-connector/dp/84K5105?_requestid=73445
I build up programming tools with these on the end, and just hold the connector to the vias while programming. Works awesome, and doesn't require a header to be soldered on there so your form factor is a little nicer.