If you have not gone out and purchased epoxy yet, I recommend several brands other than WEST SYSTEM. I prefer MAS or System Three for ease of use and no-blush characteristics. A mini epoxy kit that included the resin, hardener, calibrated pumps, wood flour, and silica powder is a a very handy package to have available in your shop for small boat projects like this hatch repair you are presently undertaking. Here is an example of an epoxy kit at a decent price:
http://www.clcboats.com/shop/products/b ... omy-4.htmlNote that the pumps included with the above kit are calibrated to dispense the correct resin:hardener ratio (2:1) by depressing each pump a full stroke once. In other words, to achieve the correct ratio you press the resin pump once and the hardener pump once.
In the case of your hatch project. I agree with the suggestion to first coat any wood that is exposed on the underside of the hatch with clear epoxy (which is to say, resin and hardener that have been combined and mixed in the correct ratio.) You would apply the clear epoxy with a foam brush, just sufficiently to coat the surfaces and seal up any exposed end grain.
To fill the voids where rotted wood has been removed, I do not recommend using silica powder as the epoxy thickener. Silica powder is often added to mixed epoxy to thicken it somewhat and improve its adhesive qualities for bonding separate components together. It helps the epoxy to grip and cures VERY hard. As such, it is not a good choice for filling voids because the very fine silica powder does not add enough "bulk" to the epoxy to create the sort of volume required for filling large voids. Also, it dries VERY hard and is difficult to sand.
Wood flour is a better choice when thickening epoxy for filling voids. Wood flour adds more lightweight bulk and when mixed to the correct consistency is easier to work with because it does not run or flow. Also, when the epoxy sets, the much less dense filler material (wood flour) will be much easier to sand smooth and fair. Mix the wood flour slowly into your epoxy mixture until it reaches a peanut butter consistency (not runny--it should stick to your mixing tool and not drip off of it.) Then apply it to your voids with a small plastic squeegee/scraper and smooth it out as best you can.
Allow the epoxy/wood flour mixture to set-up for an hour or two. At this point the mixture should not have hardened, merely become somewhat more firm in consistency. Return with a small cup of denatured alcohol and dip your latex-gloved fingers in the cup to dampen them with the alcohol. Use your fingers to clean up any run-over and gently smooth out any imperfections on the edges and surface of the void that was filled. The more clean-up you do now, the less sanding you will have to do later when the epoxy fully cures.
You can also use the epoxy-wood flour mixture to fill the voids in the other fibreglass piece of the hatch. Clean-up and smooth out in the same way with gloved fingers and denatured alcohol.
After the epoxy-wood flour has fully cured--it's usually best to let it cure overnight--sand the components with something like 100-150 grit so the surfaces are fair and relatively even.
Now you can use a mixture of epoxy-silica powder (alternatively, cell-o-fill) to bond the two pieces of the hatch together. Mix some epoxy and slowly add silica powder until it reaches a somewhat runny, mustard-like consistency. Then apply the mixture to both surfaces that will be bonded together using a disposable foam or chip bristle brush. Align carefully, then clamp the two components together and/or use weights to compress them together. Immediately clean up any epoxy-silica powder that runs out around the edges due to the clamping compression. Come back again in an hour or two and check for more run-out, and clean-up as necessary After removing any thickened epoxy that runs out from the edges, some tacky resin will still remain. A cloth dampened with denatured alcohol will clean this residue up nicely.
This is how I would tackle this project. Good luck and I hope you can use some of these suggestions.