almost all frames 1/2 full of honey

The goldenrod are starting to bloom here ,so I was going to pull some honey before the goldenrod honey.
when I pulled frames , the first deep is top 1/3 is capped honey ,bottom 2/3 is mostly brood with some pollin. the second deep is top 1/2 is capped and uncapped honey. bottom 1/2 is pollin with some brood mixed in . top deep is 3 or 4 frames that I moved up from #2 and the rest empty frames.(all 3hives are about the same )( 2 are june nucs and 1 over wintered but came out very small )
I am not to concerned about getting honey this year, I could cut out the top and crush if I want some.
my question is there any thing I could of done to get them to fill out the frames? Like not putting on 3rd deep or,putting on Queen ex. to keep all brood down and more honey up or 3rd shallow and not a deep.
I'am sure they will fill everything for winter with goldenrod