Is a symmetrical AMS 2 Pro and AMS HT set up OK or is this going to interfere with the way the Vortek system allocates hot ends depending on what side the filament is on?
right side will be slower becasue filament will have longer route to the extruder…nice setup
Wow, nice setup. I like the split shelves. I have one wide wire shelf going over the top of mine right now (with a measly one each of the AMS’), 12" deep so I can still get in the top easily. But I like your setup… and one could hook a connecting shelf between the two tops if one needed top feeding or more space. Sweet! 
Oh your question, right, sorry… 
It’s basically up to you how you assign the filaments when you send a print (or start one from the printer). You’ll get default “suggestions,” depending on where you’re setting up the print from (printer/Studio/Handy), but you’re still in control. In Studio for example you can go fully manual so it prompts you each time, or let it set up a default.
These are probably informative if you haven’t seen them yet:
https://wiki.bambulab.com/en/software/bambu-studio/manual/dual-nozzles-slicing-filament-grouping
https://wiki.bambulab.com/en/software/bambu-studio/multi-color-printing
Plus looks like you can always pick and choose which AMS tube goes to which port/hub! There are some fancy printable switchers out there, if you wanted to go that far.
Cheers,
-Max