What do yo mean by "1-2 inch rocks"? are you looking at flat rocks that are 1-2" thick, (slate, flagstone, etc.), or large pebbles that are 1-2" diameter? or something else?
If you are putting bigger rocks in the tank, I'd probably put them on the bottom, without gravel underneath them, I'd be too concerned with the gravel shifting.
One thing I've heard mentioned that people working with rocks and especially digging fish is to use some of the eggcrate light diffusers, put a sheet of that on the bottom of the tank, and then put the rocks on top- it keeps the rocks from scratching the glass and distributes the weight some.
sounds like a pretty nice sized tank for a paludarium. As to what rocks to use, it depends on what you are putting in, what plants, etc. I believe guppies do pretty well in slightly hard water, so you may not be too concerned about affecting hardness/pH.
Then again, paludariums are more prone to problems with mineral deposits at the waterline, since it's visible, and hardwater will just exacerbate this.