I would get that biocube up and running barebottom with no rocks or decorations. make sure to add something to seed the bacteria. Since you dont want to transfer any potential nudi eggs to the second biocube, dr tims, biospira, etc. could be used to kickstart the new tank. Let it run until ammonia and nitrates hit zero and do as many water changes as are necessary to get nitrates below 20 ppm (much lower is better, but corals can handle that level for a few days better than being eaten by nudis). If that nudi was a zoa eating nudi (i suspect it is) then the inly thing that needs to move to QT is your zoa colonies. If you used superglue, they should come right off with a little bit of force. They will all need to be dipped before going into quarantine. I would recommend getting a small bottle of coral rx and do a 5 minute dip in coral rx followed by a 5 min dip in revive before each frag goes into qt. They will need to stay in there for 6 weeks if I remember correctly to allow time for all nudis to die in your main tank and for all the eggs to hatch and die. After that period has passed, you can safely add them back to your main tank after a full dip and acclimation procedure without risk of the nudis coming back.