I have not assembled puzzle joints so take my opinion with a grain of salt.

I'd be wary of splintering and peeling the outer layer of plywood hammering it together.

Assembling puzzle joints 'dry' can lead to issues when they're disassembled for glue-up. Better to arrange for some means of applying even pressure across the tabs once epoxy's been applied and the joint assembled. Rubber mallet's a bit too 'focused' on a small area unless you're comfortable pursuading the joint - lubed with epoxy - into final configuration.

I'm a big fan of cauls that span the width of joints being assembled, then pressure applied by inserting wood shims between cauls and another board that's in contact with the joint's top surface. The shims are driven in slowly so that even pressure's applied across the full width of the panel.

Somewhere here a year or so back I managed to get pics uploaded that show this arrangement. If I can find 'em I'll return with a link that'll take you there.

Dept. of Leap'o'faith...

Here's a link showing how I set up for P'joints using cauls (wood member against which pressure is applied by shims) and a flat bit of wood atop a sheet of polyethylene plastic (so it doesn't get to be part of the panel... yet) that's all positioned across a panel whose puzzle joint I'm working to make as one.

Let me know if this works please. Apple says 'anyone with the link' can view the images saved to my iCloud storage allotment.

We'll see.... 

   Just finished the bottom piece of th Jimmy Skiff II. Challenge because it is bulky. Sanded puzzle pieces of both parts smooth to fit. Don't over sand. Did use a rubber mallet to check fit. Be careful taking it apart. These pieces were large. Slowly work the joint back and forth and push out each nib. Make sure the pieces are absolutely flush when it comes time to epoxy. I made a jig with  a 3x4x 1/2 piece of birch ply under the joint with weight on one side, then epoxied, Made the fit. Even though flush, one nib insisted on popping up a bit. Solution here was a strip of plastic over the seam, board, and heavy weight. I used a cinder block. Worked like a charm. BTW, don't use too much epoxy. Early lesson, but turned out fine with orbital sander 120 grit --- good luck

I'm making a Passagemaker as well.  Last week I put together all my puzzle joints, they were tight but went together once the boards were in alignment. I tried to dry fit one of the side panels just to make sure they went together before I mixed the epoxy. I quickly realized they would be a bitch to get apart. So I decided to go for it and once the epoxy was on and the boards were flat and perfectly aligned I was able to push each finger in by hand. 

I think it is best to have a long flat smooth table to lay the pieces on, so you can make sure they are perfectly aligned. I was able to push the pieces together by  hand.  I didn’t need a hammer or a clamp to force them.

   Thanks for the suggestions.  - I was able to access the link for the calls and think I understand their use.  Also, I gather the key is to fit the joints wet since testing dry after light sanding can lead to other difficulties.  I will give it a go.

   I have not done a Passagemaker. 

Most of my boats ended up with glass and epoxy on both sides of the puzzle joints. So I dry fit them by sanding so they easily fit (no mallets) and then "tack welded" the joint with CA glue. The epoxy saturation when putting cloth on does the rest.