This is what I started with - DS1054Z math to show the difference of two signals:

With the differential probe, I can get a better signal representation and get one input channel back. 

Here's a sample screenshot that actually shows what the probe does:

• supply voltage to motor: 5V, duty cycle about 60%
• Ch1: 3-state PWM input to motor phase A
• Ch2: bemf from phase A, through a 10k/2k2 voltage divider
• Ch3: virtual center (all phase feedback signal tied to a common node through 2k2 resistors)
• Ch4: Ch2-Ch3, using the diff probe

It has been a very pleasant journey into the analog world for me. Thanks Bud!