Hi Jim,
Some of my colonies are on double brood over winter. In these cases I do not leave a Queen excluder on, this allows them to move with the Queen to use food in any part of the boxes as they need it. I find these colonies are much slower to try to swarm in the spring and when they do I have sufficent comb to split them with a full brood box of drawn comb and it gives flexibility in removing old/badly drawn comb in the spring.
I would normally put the second brood box on top of the existing box after I have extracted the honey and then feed syrup to pull any undrawn comb and to replace extracted honey. As you already have a second brood box on, if you have full combs of honey which have not been used by the bees for brood, then these can be extracted first. Put the cleanest combs in the top box and all the brood in the bottom box, in the Spring you will more than likely find the Queen will be in the top box, as this will be the warmest part of the hive. Remember - no Queen excluder
The bees will collect Himalayan Balsam and Ivy to refill the comb, but always make sure they have a generous amount of stores. In September give them a good feed and aim to achieve a balance between the Queen having plenty of laying room to produce winter bees and getting the boxes filled with stores for the winter. With two brood boxes this is easier, the problem with a single National brood box is that it is very easy to block the Queen's laying area with syrup, especially when there is undrawn comb still in the brood chamber. The bees have an annoying habit of filling every cell with syrup before they draw the new comb.
If you treat with Apiguard do it when the weather is cooler. If you do it in the sort of weather we have been getting you will find all your bees outside the hive, you will also find that your Queen will probably stop laying. Treat in September when it is cooler (maybe), put an eke between the two brood boxes and put your tray in there.
Let us know what you decide to do and how it goes.
Good luck
Ruth