Does Mach3 keep the motors locked at zero speed whenever it is active? If so, how do people operate, shut down Mach when not running the machine?
This is not really a function of Mach3, unless your stepper drives use an Enable signal, and you wire those to Mach 3's Enable inputs.
Typically, when your drives are powered, they lock the motors. Some drives use current reduction to reduce motor heat when the motors are idle, but again, this is not a Mach3 function.
What I do, is start Mach3, and when it's running and out of Estop, I turn on the power to my drives.
To shut down, I turn off the power to the drives, and then close Mach3.
Your motors should never be powered when Mach3 is not running.
Home switches - my machine has two Y's, so I will have to slave to A axis correct? I think I read that you cannot series the home switches (to one input) with a slaved axis? So , if true, and I understand, I will use three inputs for the switches (X,Y,Z) and the last for my touch plate? correct?
A lot of people with limited inputs use one input for X, Y, and Z, and one for the A axis. your slave and master need to use separate inputs if you want Mach3 to square the gantry when homing.
Touch plate...my TinyG resets (to 0) the machine home when the touch plate is run...is this the way Mach works? I would thing a better way would be to leave the machine home (alone) and set the G54 Z offset to 0?!? How does Mach do it (Z axis touch plate)?
Mach3 has no default touch plate functionality. It's up to you to either find one or write your own. The vast majority (all that I've seen) just zero the Z axis (set the G54 (or current coordinate system) offset). Home position is usually set with a Z axis home switch, at the top of the Z travel.