hi pam!
this is why is is always good to have two hives rather than one, so you can learn from and compare. ultimately, and sometimes one hive will be stronger or other things that happen. it is not unusual that one hive is stronger than another (unless a problem) and it is not always necessary to find the queen, AS LONG AS, you see good laying patterns, tight solid brood/laying patterns, honey/pollen, eggs and larva. if you see these, it is not necessary to go digging in the hive to find her. if you are seeing less than this, then there might be a problem with the queen, or something else going on.
as far as when to place the supers on, your second deep needs to have the foundation drawn out, in the 2nd deep the queen will lay (if drawn out), and the bees will store honey reserves on the outside frames. are you using 10 frame deeps? the frames must all be drawn, the queen laying in the second deep, honey/pollen being filled and when you see they are getting to the point of running out of room, then add a medium super.
as far as extraction and what get's saved for overwintering; i usually take all the supers off once a season, in late august/early september. sometimes in dearth the bees will utilize the honey packed away in these. i overwinter in deeps only. i make sure the hives are heavy before going into winter months, either feeding back to them frames of honey with too high a moisture content; and also adding a shim and feeding fondant/winter patty if necessary.