I know that one has high gain and the other is the lower output but can anyone tell me more about these two inputs and how you would go about using them?

I haven't really had the time to crank my amp yet but it sounds as if the low input does not distort too much. Is this true?

And for my last and most important question...I heard that the low input of a JCM 800 is supposed to be exactly the same as that of a 1959 SLP Plexi. Is this true at all? If so I shouldn't have any problem getting some sick plexi tones out of my amp right?
you will recieve much more help in the Guitar Gear and Accessories forum.

I believe you are right, the 'low' input sounds much like a Plexi. It won't sound 100% like a Hand Wired 1959, but as far as the 1959 SLP goes, it should.