Excerpt from Tim Lackey on the Plastic Classic Forum:

Here’s what I’d do for any fastener; this assumes that steps to isolate any core material have already been taken.

1. Drill hole just undersized to allow for use of a tap to thread the inside of the hole. Threaded holes not only hold the fastener more securely, but they make installation much easier–particularly alone.
2. Mill a countersink at the top of the hole. This creates a nice pocket for additional sealant to collect right where it’s needed most–around each individual fastener. It takes 2 seconds with a countersink bit in your drill. I’ll often have three drills going for installing hardware: one for drilling the pilot hole, a second containing the appropriate tap bit, and the third with the countersink.
3. Mask over the area, temporarily install the hardware, and draw the outline on the tape; remove the center portion of the tape as needed.
4. Gob on the sealant, being very generous and ensuring that plenty ends up around all of the fastener holes. There’s no such thing as too much sealant. It may seem wasteful, but one doesn’t want leaks.
5. Install the hardware and tighten the fasteners securely from the top; the tapped holes will allow the fasteners to pull the piece right down nicely.
6. At your leisure, go below and add backing plates, washers and nuts as required. You can tighten these from below without needing to hold the screw from above.
7. Either leave the sealant to cure for a day or two before peeling away the cured excess (large amounts of squeeze out can take a while to fully cure inside), or clean it up using solvent. Either will work; one is far messier than the other. I have done both ways; I’m not sure which I prefer. Often, it depends on the situation. Sometimes, gobs of partially cured sealant can get in the way of other projects or something, and it’s better to just get rid of it. Other times, leaving the beads for a day or more is no problem.

Using masking tape keeps the surrounding deck pretty clean either way. Often, I will use a squeegee or something to remove the bulk of excess sealant, peel away the tape, and then use solvent to clean up the minimal remains. This way, the job is just done.