Firstly you need to get the two hives you want to unite within about 4 or 5 foot of each other. If this is already the case then great if not you can move both of them about 2 foot towards each other each day (assuming the weather is good). Newspaper method works well but to be honest all I do is once the hives are close enough then put the decent hive in the middle of where the two were. Smoke the rubbish hive well (so that they fill up on honey) then take it away about 50 yards and shake all the bees onto the ground - they tend to sort themselves out without much fighting. Sometimes they can form clumps on the roof or ground around the new hive so go back after 20 mins. and smoke them off if necessary, they usually seem to go in ok after this.
I would bin the drone brood, it will be full of varroa and will only be a drain on the hive. Not a real fan of double brood box methods but then I mostly use langstroth jumbo equipment.