.... I set the swarm on top of a hive that I think is queenless. I will combine the Sat when I pull my first honey harvest.
If you can be sure that the bottom hive is queenless, don't wait with the merger.
1. You'll avoid the problem of possibly developing laying workers.
2. You'll have a stronger hive to bring in a bigger honey crop.
To prevent the problem of brood in the honey frames, make sure that after combination of the families, the queen and any brood she's started in the upper box get moved down.
If you believe in using queen excluders, this would be the time to put one on to keep her down below. You could set back the top super about 2 cm (an inch or so), to make it easy for the field bees to enter the top super without having to go through the excluder to deposit their nectar. When the honey flow ends, move the super forward so as not to inspire robbing.