To prevent stromboli from becoming soggy you need to make sure to cut the slits in the top of the stromboli. This will let the steam escape while it bakes. If you use a meat with a lot of moisture like ham or canadian bacon, drying it off with a paper towel to remove excess moisture before adding it to the stromboli will help.  Another trick is to cook it on a preheat pizza stone so the bottom becomes nice and tricky.