Hi,
I cant tell you much about a WarpRunner, but I have used an ESS and Mach4 for 8.5years.

A G540 is a combination breakout board with four stepper drivers built in. It has 'one ports worth' of IO, ie 17 inputs and outputs. As 12 of them are outputs that leaves only five inputs.
You would need at least one of those for an Estop. You are advised not to hook any switches or other paraphernalia to the ESS, not because you can't, but any small cock-up and you'll
blow the ESS. If you use a good breakout board, any cockup might wreck the breakout board but not the ESS.

The issue you have is that you really only have four spare inputs. If you got a second breakout board like a C10 ($23.00) then you have 'two ports worth' of IO, one from the G540 and the other from
the C10. The second port of the ESS you can direct it to make pins 2-9 (of port two) inputs, thus you would have a total of 18inputs and 16 outputs....much more useful.

I made my own breakout board because I wanted features that suited the servos that I used on my new mill. It uses all three ports of the ESS for 51 IO's in total with 31 inputs and 20 outputs.
The motor outputs (step/Dir) of all six axes are differential (for high speed signaling to servos), a relay and PWN outputs for the spindle, and a 24VDC output for the electromagnetic brake on the
Z axis. The remaining inputs are 24V active low, and the remaining outputs are 24VDC sourcing and sinking.

So specifically:
Do you hook up the limit switches to the gecko or the SmoothStepper?
Do not hook direct to the ESS, hook to spare inputs of the Gecko and/or spare inputs on your C10(recommended)

Going to hook the gecko to the SmoothStepper and SmoothStepper to the computer via Ethernet cord.
Yes, that is correct.

I also read that you should also hook up the EStop to both gecko “and” the SmoothStepper, is this correct?
No, the Estop is hooked to a spare breakout board input (either G540 OR C10) and that signals the ESS.

Here is the biggie. What is the proper way to hook up EStop and limit switches when I add the WarpRunner?
Don't know......I believe the WarpRunner replaces both the G540 and the C10, ie it is a fully developed three port breakout board that has in addition to all the usual
breakout board features it has THC features as well. The Warp9TD forum is the best place to get this info.

Craig