Taking off an Extra Brood Box

[Swift Nick]

I had a hive with a double 14 x 12 brood box through the winter, it was like that because I was using a Cloake board between the boxes for queen rearing. I was planning to remove the lower box in late February when it was most likely empty, but it didn't happen. Now the queen has laid in the upper brood box, but also a little in the lower brood box. Last weekend I swapped the boxes and put a queen excluder between them, today I confirmed that the queen is in the (now) lower box with the majority of the brood. Bees have been filling the upper box with nectar.
I want to get the hive back to a normal configuration, one 14 x 12 brood box and add supers as required.
I was thinking of putting a super over the queen excluder, but under the upper 14 x 12 box, then when the small amount of brood in the upper 14 x 12 box has emerged, use a clearing board overnight to get the majority of bees out of the upper brood box into the super or lower brood box.
(1) Has anyone got a better way of doing this? am I over complicating it?
(2) when I get the upper brood box off what is the best thing to do with the combs? can they be stored or will the nectar the bees have been bringing in ferment?
Any suggestions welcome, thanks.

 

[Ian123]

Now you have the queen in the bottom box simply put any frames with brood from the second down with her. You can reserve any filled with honey for nucs\swarms.