Glad you're making progress and congrats on your good drain idea. Here's an extra thing to check: When installing my inspection port under the porta-potty it rained, and suddenly there were active leaks under the fittings for the factory's front rails and bow cleat, and also around portlights, windlass and antenna cable added by the previous owner. Clearly they'd been leaking rainwater for a while. Removing and re-bedding all those fittings (mostly with butyl tape sealant) was a (sort of) fun project and fixed the leaks. With that and a good boat cover (try Empire Covers), the under-floor area has stayed dry. So take a good look for leaks ... the water may be coming from above, not below!
In fact I discovered wet core around several of the fittings, which gave me another opportunity to excel....
Finally, to answer your question about installing things in anti-skid, it's safe and easy to grind down the anti-skid nubs with a Dremel until you have a flat surface exactly where you need it, then install bedding and the item itself.