The projcect that I run in SQLPackager is a script created by SQLCompare after comparing a scripts folder of objects(all create scripts) against an empty database. Therefore what I'm packaging is already a big create script.
I did just try to add a create db script that I use when testing the sync script that I get from SQLCompare. I still only get the option to upgrade, but I am able to choose the master table as my table to update and everything runs as I would like.
It wasn't the end of the world or anything, but is always nice to be able to get what you want.
Thanks for all your time David.