I set up a performance with a split for bass on the left hand and piano on the right. I then set up the sixteen parts with other sounds. I then start the rhythm pattern.  When I press the part select button, the split light goes out and whatever part I programmed is on the whole keyboard, and I lose the benefit of the bass on the left split. 

On the other hand, if I just press the part buttons without pressing the part select button, the keyboard plays the factory installed voices which are not always sufficient or desired.  If I change the performance, the rhythm pattern stops. I don’t think Yamaha thought this through when they designed the MX61 because, to me, this is a serious limitation.

My question is this: Is there some way to start the rhythm pattern, press the part select button, and switch between the part sounds I want while maintaining the split or is this just a limitation of the keyboard?

First of all, when you start the rhythm pattern in a specific performance and then you press the part select button and you switch between different parts, the rhythm pattern does not stop. The rhythm pattern stops either when you press the stop button or when you select a different performance.

The second case (to maintain splits while selecting parts) is more complicated. The onboard split/layer buttons is a quick way to layer/split only parts 1 and 2 (or more accurately midi channels 1 and 2). So, either in part select mode or not, with those buttons you can only layer/split only the first two parts in each performance. When you move to a different part, no layers/splits exist.

What you can do to overcome this situation is trying to create performances by using a performance editor program (either John Melas performance editor or the VycroMX editor). With those editors you can create very complex performances with any kind of layers/splits/velocities between the 16 parts of a performance.

Here is an example:

Use a bass voice in part 1 assigned to midi channel 1 layered above C3.
Use a piano voice in part 2 assigned again to midi channel 1 layered below C3.
Use the same bass voice in part 3 assigned to midi channel 2 layered above C3.
Use a string voice in part 4 assigned again to midi channel 2 layered below C3.
Use a drum kit voice for part 10 assigned to midi channel 10.

Then when you select part 1 in part select mode, you will have a bass and a piano split in C3. And when you select part 2,you will have the same bass and a string split in C3. The rhythm pattern uses part 10.
If you press layer/split buttons, the result is a combination of all the above.
The possibilities are endless, if you use the rest of the 16 parts. The secret is to use the correct midi channels and make the correct splits/layers across the keyboard.

The only disadvantage to the above workaround is that you cannot not see the correct voice names when you select the various parts (you have to remember what voices you have used in each layer/split).

Thank you Kostas.  That sounds like a great idea using the midi channels anf the Vycro editor. I will try that.

I tried assigning the various voices with the bass to paired midi channels. For example- piano/bass to channel 1, organ/bass to channel 2, etc. on the Vycro MX editor, but I wasn’t able to store that performance on the keyboard even if I first saved it to an external disk because it was a different file type than the keyboard performances. 

What I am trying to do is play various sounds with the bass on the MX61 within a same performance while maintaining the split and drum machine.  Right now, I can press the part select button and get the right hand sounds I programmed with the drum machine going, but I lose the split for the left hand bass.  If I don’t press the part select button, yes I can maintain the drum machine and split, but when I press the various part buttons, they all default to 001 of that particular category so that is useless for me especially at a gig. 

I already have a higher end Yamaha keyboard that will allow me to play its drum machine with splits and voices of my choosing.  I was hoping to use the MX61 as a backup in live performances, but I think Yamaha missed the mark in that category.  So basically I am limited to using the MX61 as a second keyboard to switch between right hand sounds.  Maybe Yamaha could fix this limitation with a new firmware.

I think something you are doing wrong. In Vycro MX editor (the free version) when you finish your editing, you use the onboard STORE button in order to store your performance in your instrument (there is no store option in the software, only save option to disk). In John Melas Performance editor there is a store option in the software editor, but it has a bug and in some cases it doesn’t transmit the changes. In any case, with both software editors you can make all your edits in your computer and then use the onboard STORE button to store your MEGA Performances on the instrument’s internal memory.

What I have described above is completely feasible with both software editors, it has been tested and verified by me and it is the only way to achieve what you have in your mind (if I have understood it correctly).