If the queen came marked, its unlikely that the markings would come off in just a few days. Also it is unusual that you see drone brood just a few days after a queen has been introduced to a colony that's been queenless for a while - even more so at this time of year.
In my view you don't need to bruise the cappings - the bees have space so they will move stores around as they need. As there are plenty of stores and a laying queen - doing nicely, then there is no need to mess with them - they should be left alone for 7 - 10 days to allow themselves to organise the brood nest as they want.
Bees have been keeping bees for a lot longer than we have.
Test Frame: A frame of brood with eggs and small larvae is placed in the hive. If there is no queen the bees will try to raise one so you'll see queencells after a few days. If there is a queen, then no queencells will be produced.