I feel like we're talking about sheet aluminum here, in which case you don't want to tap it. Generally speaking, you only want to tap a hole (in any material) if the material thickness is at least 1.5 times the diameter of the screw. (In a pinch, with light load, 1.0 times the diameter might be okay.) That's unlikely to be the case with sheet metal.
If you're using self-tapping screws in sheet metal then, yes, you just drill the hole and then drive the screw in. In a soft material like aluminum, I generally make the pilot hole just slightly smaller than the root diameter of the thread on the screw.
I'm not a huge fan of self-tapping screws in sheet metal, though. They're fine for a quick and dirty job, and they're also fine for a joint that carries little load, is not mission critical, and will rarely be undone. If it doesn't meet those criteria then I find a different solution. Since I also find separate nuts annoying, I like to use a plate nut (sometimes called a "speed nut") or some kind of fixed nut, such as a rivet nut or swaged nut. It's more work up front, but you'll thank me later. If you don't expect to have to take it apart very often (i.e., probably never again as long as you own the boat), then nuts are fine.
