Keeping temps of substrate right.

[Craiga 01453]

Perhaps this is where I'm confused as a new keeper. Some people use no substrate, keeping the same temp with paper, while others use 2 inches of stuff.

They would differ drastically in this case, no?

Nope, regardless of substrate you want to focus on just the surface temps.
You also want to monitor ambient temps. Your cool side should be around 80, but no lower than 75