This, from their literature-
"4. Q: Can I use Apiguard with a brood and a half or a double brood?
A: Yes, but bear in mind that the level of mite control may be slightly lower than with a single brood chamber, as the number of bees that need to receive treatment is higher.
Most bees, brood and varroa will usually be in the lower brood chamber, so place the Apiguard on top of the brood frames of the lower chamber and put the second brood chamber
on top (ie the Apiguard is between the brood boxes). Repeat after 2 weeks, following Point 2 above".
However I think that label instructions are law, any other advice is advice.