if your purpose is to give the queen more room, you need to give her a clear space to move up/down as they build comb. she won't cross the honey at the top of the brood most of the time. in that case, i would do as iddee says and put the boxes under.
if your purpose is to give them room for honey, there must be a flow or they will not build comb or store. in fact, i have found that by feeding when there is no flow, they often will backfill at a faster pace rather than build the comb i want.
they are getting to the time of year that storage is on their mind so you will have to balance that against leaving the queen enough space for her brood.
don't worry about the burr comb. don't worry if they build some from the bottom. they do that on occasion. make sure your frames are together to help avoid cross comb. i know people go with fewer frames in the honey supers and that's great, but if you are getting foundationless frames built out, you need to keep them tight until they are done.
JackM has a good suggestion if you are putting honey supers on top. move the outside frames, if they are empty, closer to the middle if they are not full of honey. this will give the queen clear space to move up and give her more room to lay. if they are full....no good.