Figured out my problem thanks to Soren. Turns out you have to have two systems in a constellation for it to show up. IMO I should be able to create arbitrary one-system constellations, but whatever.
For future reference, here's a partial code example that covers the essentials of adding a constellation.
// Create the constellation
Constellation constellar = new Constellation(ConstellationType.NORMAL, StarAge.AVERAGE);
constellar.setNamePick(new NamePick(new NameGenData("null", "null"), "Constellation Name", null));
// Get the systems, or generate them in this case
StarSystemAPI xSystem = XSystem.generate(sector);
StarSystemAPI ySystem = YSystem.generate(sector);
// Add the systems to the constellation
constellar.getSystems().add(xSystem);
constellar.getSystems().add(ySystem);
// Yes, you have to link both ways
xSystem.setConstellation(constellar);
ySystem.setConstellation(constellar);