Welcome to the forum!

Disclaimer - we don't have access to a YC and you don't mention which model you have so the comments below are based on experience with using Yamaha's organ sounds on later models.

it's hard to just do a "set it and forget it."

The hardest thing for users (but maybe not you) to wrap their heads around is that few, if any, of Yamaha's instruments fall into the "set it and forget it" category.

Virtually everything they do happens because of their programming: either embedded in the presets or programmed by a user.

The YC sounds are no different in that regard.

I play lots of different types of sounds across a music set (Pianos, EPs, Organs, DX sounds, etc.) that my frequency ranges are all over the place

Most presets are designed to DEMO what the instrument is capable of and aren't necessarily ready to use 'out of the box' in any particular venue setting.

For what you describe you will often need to use several 'tweaked' versions of the same preset for them to fit into the different acoustic environs you mention.

So our first advice is to approach the task with that in mind: select a preset and work on modifying it for a particular set of acoustics. Save that as your own sound. Then take the same preset and modify it for a different set.

One might need to have the bass emphasized while another might need emphasis on chorus or 'pulsing' of the sound to make its presence known.

Make sure the bass frequency of the rotor is actually being used - it might be off or set too low. That is an area where EQ can help you quite a bit.

Try different rotor a/b settings. They each have different 'default' charateristics.

Increase the 'drive' setting - but not into the hard distortion range. That adds some additional harmonics and those can better 'fit between the gaps' that other instruments (guitar, bass, keyboard) might leave. The sound you put in those 'gaps' will be more noticeable the more they are different from the sound before and after the gap.

I'm looking for some guidance in integrating all the great sounding organs from the YC into a live setting. 

SUMMARY

#1 - always have the most control of your sound that is possible.

#2 - Tip #1 means NEVER use presets - always use your own 'tweaked' version of a preset so that you know for certain exactly what it will do in any playing venue/environment. That might mean having 4 'different' versions of the same preset and switching between them when the next tune comes up.

To be sure - we get a LOT of initial negative reactions about tip #2. Many musicians just want to play - they don't want to spend their time programming. They get that 'warm, fuzzy' feeling when they can just buy an instrument, rip open the box, plug it in and start making music.

Unfortunately Yamaha's synths don't really fit that paradigm. It isn't a real good analogy but might help get the point across. Most guitar players take multiple guitars to a gig. Sometimes they need acoustic, sometimes electric. Often they will bring their own amps or effects.

You need to do the same with your YC and any given preset. Do testing ahead of time and create your own organ sound that emphasizes the bass over the treble or pushes the limits of drive/distortion. Build your own 'toolkit' of sounds. 

Once you know how to tailor a sound for a given venue it will be easier to do those 'tweaks' on other presets because you will know what to look for.

Sorry we can't be more specific - but hope the above helps some while you wait for someone with specific YC experience to respond.