I now have one deep with two mediums on top. I want to go to two deeps. I dont want to miss the flow that starts in a couple of months. How do I get to two deeps? Should I wait until after the flow when I start feeding sugar syrup so I dont have an empty box while trying to make honey during the flow?
Man I hope this makes sense!!
Dale
It does to me! 
OK, take a deep breath and slow down. You can do this, and so can your bees. 
On another thread, you say that the 2 mediums are filled with syrup stores. That implies that the bees may be short of space already. I am a little unusual (just ask my husband), but I would buy and construct another deep box and place it underneath your existing boxes. The reasons are many, but the queen usually prefers moving down and putting more brood in a box below her existing box. If you don’t want to impact this year’s harvest, that is what I would do.
When the nectar flow starts, you can remove one or both mediums (extract and/or freeze them for at least 48 hours), and then use them for feeding the bees next fall/winter. Then you just put the Flow super on top and don’t get syrup in it. 
Easy peasy, you can do this!