Okay. So I’ve got a step track for drums with x instruments and want to mute sounds live within that track. Possible? I know I can mute steps or make x amount of tracks with single instruments and mute those, but that’s precious real estate
You have 64 tracks. Sixty. Four. I wouldn’t worry about tracks being such a scarce resource.
Personally I use the following layout:
BankA ( 16 tracks ) is for Drums. within those tracks I have certain instruments that are by themselves on that track, because I want to be able to mute them ( Kick, snare, clap, whatever ) and other that are on the same track, but with variations in the patterns of that track. For example the 3-4 sounds of a conga are on the same track because it doesn’t make sense to mute those separately.
BankB is for synths. I usually cluster track together by use, and sometimes dedicate 2 tracks to the same instrument, so I can have overlays ( core notes on a primary track, alternate flourishes on an overlay, so I can use a differen length or completely different MidiFX )
My default layout is:
BankA: drums and percussion
BankB: synths
BankC: overflow from A/B
BankD: WIP and non-performance related items ( like tuning for analog voices )
Do you often run out of tracks in your projects?
I definitely see your point. It is just more button than I would like. I am used to having to conserve tracks. Writing a drum pattern is a lot easier (and fun) on one track than spreading them out. Also when writing a set with 12 songs at ~minimum 6-8 tracks per song… Well yeah.
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Drum parts should be on different tracks. Once you get into patterns you will understand that it make more sense.
So if you want your hats to do something else you dont have to change everything, just the hats. 
Ah us, patterns, I’ve yet to explore that. I imagine I could mute a track, switch the pattern, then bring is back with the change up. That said I could see using 64 on a live set given 12 song at 5 synth+ 6 drum parts, but that aside from the conversation. I just see myself accidentally muting the wrong parts😀
You can name tracks and then save the layout.
I always have the kick (and all other drum parts also) on one specific track across all projects.
So I can simply change the kick pattern while keeping everything else the same or mute the hats etc. 
Personally I find that having the entire set in a single Pyramid project too limiting, so I’d rather think about how I would transition projects using various devices ( droning, samples, looper ) and have at most 2 songs on the same project assuming that I wanted a very long evolution from one to the next.
I also like the muscle memory of knowing which pages contain which instruments, and being able to mute/unmute the right parts in a live setting, rather than having to track too many things in the same project. ( also I don’t compose that way, and I feel that merging would be too much work )
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I like having a looper in the mix to record a longer loop and then crossfade over to the new song.
I was just asking google the same question as the OP, and this is a great answer. A few others have said similar also - great shout you lot, thanks!
the squarp can output clock while it loads files. It’s possible to play a continuous set without putting all the songs on a single file. Just in case you didn’t know. So you can use all 64 (plus patterns) for a single song, if you want. That said, there can be some nice benefits to having multiple songs in a single file too. Anyways, just thought i’d mention that in case you hadn’t heard that yet.
+1 pretty much everything you just said. I approach mixing between songs on the pyramid this way too. I have other sequencers play a part or two while I pop a new song file on the pyramid.
And, the muscle memory thing I think is super helpful - I have a template I work from and page A is always instruments with a specific layout, page C are my sequencer trigs, and page D is my visualizer output (just for example). I think its well worth putting time into what your workflow is gonna be and that can be tough if you’re trying to shove a 12 song set onto a single file (but not impossible).