Press the Home Button - then Audio Routing - then SD Card/USB/AES.
Under the SD Assign Channel 33/34 you can assign any of the following to record on to channels 33/34:
Any two of the 16 Flex Mixes in pairs - that is (1/2 - 3/4 - 5/6 and so on)
Subgroups A/B OR C/D
Say you had the Matrix you want to record assigned to Mix 1 & Mix 2 - just assign it to Channel 33/34 on the SD Assign screen and that is what will be sent to the recorder channel 33/34.
BTW - when you select the channels you want to record to the SD Card you will arm the "MAIN" button on the screen. I know it may be confusing but if you have designated Mix 1 & Mix 2 as your Matrix and then sent it to channel 33/34 then this is what will be recorded on to the MAIN Track.
Keep in mind that you can record up to a Maximum of 34 channels to a properly configured SD Card. That is Channel Strips 1 thru 32 PLUS what ever you have assigned to channel 33/34.
Hope this helps!