Go to the Mellens website (USA) where all the service manuals are as pdfs, and look at the files for HVAC (Heating Ventilation Air Conditioning). Everything you might need to know and a lot more can be found there. Bear in mind there will be some left to right transposition on some aspects because it is specific to the LHD Miatas rather than our RHD MX5. Fortunately most of it is common to both and the principles apply equally.
http://www.mellens.net/mazda/Mazda-Miata-2006-2007/index.html
I’m prepared to bet you somehow managed to disconnect one of the plugs to the assorted motors that operate the fan and the flaps on the central box, or did not fully reseat the centre-console panel carrying the control knobs.
Good luck.