Water retention will depend mostly on how you weld, not where the patch is.
If you set it on top, and weld it from the bottom, you're sealed from rain
spray,
but wet carpet would seep water under the seam. Visa-versa if you set the
repair pan underneath.
I would encourage you set the repair pan in from above. It's quite a bit
stronger
to mount it this way (don't discount the strength aspect), and its far easier
to get
it aligned correctly as gravity will be working with you instead of against you.
At the risk of creating a firestorm, use rivets to set the pan in position.
This is
an accepted professional practice of high quality body workers. Though they
tend to use the far more expensive panel pins. Take the rivets out as you weld
along. The rivets will alo hold the panels close to each other, making for
better
welds.
Before you go glopping asphalt or waxoil or other sealants into the gap after
you
finish welding, I'd suggest primer and a paint to cover the bare metal.
Lastly, you say this is your first MIG welding job? Have you practiced enough
to be able to run good beads, and to understand how not to warp the heck
out of the replacement floorpans and the body tub? If you've got visions of
just running a bead around the replacement pans, I'd strongly encourage
you to not do this job yet. Welding body panels on properly so that you don't
do more damage then you already have is not simple, easy or intuitive.
Doing a floorpan job is an easy way to pretty well destroy a body tub through
warping.
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