The Santa Maria is one of the most popular ship modeling subjects in history - and in view of her historical importance that makes sense. Unfortunately we know virtually nothing about her. About the only primary source material is Columbus's journal. Historians and modelers have been combing in for more than 500 years now looking for tidbits of information about the ship. What they've found can be summarized quite briefly. She was, according to Columbus, a "nao" (as opposed to the "caravels" Nina and Pinta). She was the largest of his three vessels. He mentioned the number of men in her crew (which I've forgotten). And in one entry of his journal he mentioned that "I let them set all the sails: the spritsail, the foresail, the mainsail, the main topsail, the mizzen, and the boat's sail on the poop deck." That's it.
"Nao" is Spanish for "ship," so that word doesn't help us much. Quite a few historians have suggested that she was a carrack - but even that isn't known for certain. We don't know how big she was; in fact we have no knowledge of any of her dimensions. Several archaeological expeditions have gone to the Carribean over the years looking for her remains, but so far they haven't found anything.
Some people think this paucity of reliable information means we shouldn't try to build models of her, because, by definition, the models can't be accurate. Others (including me) disagree; they think speculative reconstruction projects like this are extremely rewarding because they allow for lots of individual interpretation. If ten models of the Santa Maria all look dramatically different from each other, this line of thinking goes, so much the better - as long as all of them conform to the available historical evidence.
Quite a few expert modelers and historians of naval architecture have tried their hand at reconstructing the Santa Maria. To my knowledge the best and most recent such effort is a book in the Conway Maritime Press's "Anatomy of the Ship" series, The Ships of Christopher Columbus, by Xavier Pastor. That book contains remarkably detailed drawings of Mr. Pastor's reconstructions - including rigging, internal arrangements, and everything else. Unfortunately it's been out of print for several years. Used copies show up on the web, but they aren't cheap.
Another fine artist/historian who took a crack at the Santa Maria is Bjorn Landstrom. Quite a few years ago he published a beautifully-illustrated book titled simply Columbus. It contains Landstrom's own drawings and paintings of his versions of all three ships. That one's also out of print, I'm afraid, but easier to find than the Pastor volume - and probably a bit cheaper.
There are dozens of books about Columbus, of course, but if you want to read up on the subject there's one that, to my notion, stands out above all the others: Admiral of the Ocean Sea, by Samuel Eliot Morison. It's more than fifty years old now, but anybody interested in Columbus really needs to read it. Morison, according to lots of authoritative people, was the greatest American historian of the twentieth century. (He had the rare distinction of getting a U.S. Navy warship, a Perry-class frigate, named after him.) In my personal opinion this was his greatest book. It's the product of extremely intensive research, and Morison had the reputation of being one of the best writers ever to get a Ph.D. in history. The book was a best-seller. Used copies of it are easy to find on the web - for reasonable prices. (It appeared in two forms: 1-volume and 2-volume. The single volume edition will be fine for any modeler's purposes.)
Morison discusses all the information that was available in his day (the 1930s) about the three ships, and includes very interesting chapters on navigation and life at sea. When it comes to such questions as how the ship was organized and sailed, and where people slept, Morison is an excellent, readable source. (If I remember correctly, he thought the sailors - except the officers, who had individual cabins - slept on the deck wherever they could find the room.)
As for the ship's boats - Pastor and Landstrom probably include some general guesses as to what they looked like, but that's the most you're going to find. Prior to the twentieth century there were two basic ways to build a wood boat: carvel and clinker. In clinker construction the hull planks overlap each other at the edges. In carvel construction they don't; the builder shapes the planks so the edges butt up precisely against each other. (It may sound like clinker construction is easier, but it really isn't. In order to keep the boat from leaking the edges of the planks have to be rabbeted - and the rabbet has to taper in width toward the bow and stern. Watching a good boatbuilder plank a clinker hull is fascinating.) Both methods seem to have been in use in western Europa during the late fifteenth century.
I haven't looked at the Heller kit in years, but it sounds like the designers intended to represent carvel-built boats - and didn't bother to indicate the edges of the hull planks. There's a practical reason not to do that. Even if the boat's hull is molded in two halves, the planking seams create a problem with undercutting - whether they're raised or countersunk.
I don't think any of this has helped much. With the Santa Maria, for better or worse, the modeler is largely on his own. Good luck.