I confused myself. My HVAC control is on the bottom as shown and I pictured my setup while reading your issue. I thought you wanted to install single DIN flip at the bottom bay while moving up the HVAC at the same time which to me made no sense
. There are several uses for the 3rd bay. CD storage tray, cassette tape storage (yes I know), storage cubby, HVAC, and temp gauges.
Your HVAC climate control is at the top bay from factory. You need to do pull the wiring harness down to the 3rd bay which shouldn't be too hard. Most with your setup want to bring it down to where I have it from factory. I heard that it was a very tight leash. By having the HVAC at the bottom bay it looks more uniform. It's like the two cubbies at the bottom like your setup or radio/cubby/cubby/hvac.
I suggest you remove the entire lower cubby storage. It's 5 mins total. Wear some gloves or your hands will be scuffed up.
https://rennlist.com/forums/attachments/996-forum/1029276-climate-control-relocation-mk1-img_3393-1-.jpg
Here's a thread that might help you with more pictures when jaykay did his relocation.
http://986forum.com/forums/performance-technical-chat/78248-hvac-radio-relocation-harness-route.html