The beans will have expanded after soaking, so make sure they’re still covered by the soaking water, but not by very much. Add the onion halves, Parmesan rind, and thyme to the pot and bring to a boil over medium-high heat; keep at a boil for 10 minutes. Then partially cover the pot and reduce the heat to keep the beans at a gentle simmer—medium or medium-low heat, depending on your stovetop. If the water level drops below the beans, add hot water from a teakettle to just barely cover them again—don’t add too much!