One thing to remember when assessing stores for overwintering, bees fill the combs from the top down but use it from the bottom up during cluster periods. They also tend to cluster at the top of the brood box, so if a 3rd super is used and it never had brood it it the bees will cluster below it. I have one hive I fed to bring it up to proper winter stores that is like that no cluster above the 2nd medium, the other one had brood in all 3 medium boxes and cluster right under the top.
Both of you indicated that I should take out one of the deeps resulting in a 2 deep hive. I'm assuming I should sort thru the entire hive (all 3 deeps) and remove any empty frames and recompile the remain 2 deeps with frames of honey or brood (if found). Brood frames would be placed towards the center of the top deep and honey frames on the outer perimeter of the top deep and center of the lower of the two deepss.
If I can not find enough frames with honey or brood to fill the 2 deeps, should I place frames with empty comb in the upper deep for the Queen to lay eggs?
You understood correctly, you want to have at least 1-2 frames of empty comb or par stores part open comb in the bottom super for the queen to begin laying for spring build up.