The seat screws are between the seat and pillion. There is one cap (allen head) screw on each side (two screws total). I used a long metric hex wrench (purchased as a set at Sears - great tools). In this photo, the end of the hex wrench is in the cap screw. You might have to turn the hex wrench with pliers.
There are more photos of the seat screw and sub-frame in the Sissy Bar Mounting page.
Removing the Honda VLX Seat (VT600C)
A wider angle shot of the location of the right seat screw (there are two screws - one on each side). We're looking at the right side of the bike, from the rear. The pillion pad (passenger seat rest) is in the lower left of the image. When this photo was taken my bike still had a sissy bar, and that's the chrome bar below the hex wrench.
Shadow seat mount, without the seat. This is the rear frame and fender, under the seat. The screws go into the side of those mounts sticking up in the middle of the photo. I think the seat also slides under some clips towards the rear.
In order to make the screws easier to remove later, I bought longer screws (they are metric cap screws) and a steel bushing. This allows the screws to tighten down, but extend them to make it easier to reach for removal next time. If you aren't confident in your mechanical abilities for customizations, I recommend you stick with the stock screw.