Only BeatStep "knows" that it's using a different memory.
And different memories are used exactly to use different setups i.e. different CC numbers on knobs as if you had 16x16 (256) knobs. Same for Pads
Problem is, there's really only 128 available CC's in the MIDI spec and you can't (shouldn't) use all of them, because some have special uses (like CC 00 is used for Bank Selector, CC 01 is for Mod Wheel, CC 02 is Breath, etc), so in truth you can use up to 8 memories just for the "CC extending" purpose.
So, to directly answer your question, the way you'll be able to have a set of 16 knobs for purpose A and another set (memory) for another purpose is to set each knob to a different CC.
As an example, you should set Knob 1 to 16 in Memory 1 to CC 01 through CC 17 (skipping CC 07 that's usually used for Volume, so set the big knob to CC 07).
Then, for Memory 2, set Knob 1 to 16 with CC 18 through CC 33, and so on for the other Memories.
Hope this is helpful
PS: Of course, if you use MIDI Channels, then you can really go beyond the 128 CC limitation, getting 16x128 (aprox 2048) CC possibilities.