Is there one, or two suction pipes that run back to the pool pump? I.E. 1 suction and one Main Drain, or one skimmer/maindrain line.

All,

In front of the pump, there is a 2-way valve that lines the pump either with the main drain or the skimmer. On the main drain side, there is only one line. On the skimmer side, there are 2 lines (one to each skimmer).

"Opened the drain cleanout in the skimmer" ... The skimmer has 2 holes, one that leads to the pump and one that leads to the main drain. The one leading to the main drain is normally has a plug in it. I opened this one to run a hose to clean out the drain at the bottom of the pool (it was full of stuff). I accessed the main drain line at the pump by removing the 2-way valve and running a snake down this line. No spa.

Hal

If you have a direct line from your main drain to your pump suction manifold there is no reason for that line to be plumbed in any way to your skimmer. I have never seen a "drain cleanout" like you describe.
I tend to think that either the pipe marked main drain is actually, as suggested earlier, a dedicated vac line in the wall that has a plug in it or your main drain is plugged (as in on purpose) for some reason. If someone put a plug in the main drain port in the skimmer it was either because it was never connected or both ends were plugged for a leak.

My flow diagram shows the second skimmer port to be connected to the main drain, as shown in the second diagram in the following link.

http://www.haywardnet.com/products/Manuals/pdfs/manual56.pdf

What you are showing is the method to plumb the maindrain if you do not have a dedicated line to your pump.You would not have both hooked up. Or I guess I do not know why someone would....How do you Vac your pool manually?

I have to re-read all of this. In the meantime, most pools are not plumbed with a line to the MD unless they are commercial or about 30 years old. A two skimmer install typically has one skimmer plumbed to the MD through the skimmer and it can only be diverted with the float valve in the skimmer or a manual diverter but those are two different skimmers. I'm still guessing a dedicated line for a suction cleaner. How old is this pool?

"I have to re-read all of this. In the meantime, most pools are not plumbed with a line to the MD unless they are commercial or about 30 years old."

I suppose it's all about where you are, in Seattle, most pools have dedicated lines for both the skimmer and the main drain.