Question 1: Which color plate, C, M, Y or K, or some combination of all
four? Composite printing is *entirely*different...

Question 2: You're seeing knockouts which should appear in the separations.
Otherwise one color would overprint the other and would change the
appearance of the two inks. Now maybe you want it that way for a specific
design effect. But generally overprinting is only reserved for black ontop
of another color. So it should be that way. Remember, inks are transparent,
not opaque. Only metallic inks are opaque.

I am doing a two color job black and PMS color
This is a two part question: 1. My photos are designated as grayscale, but
are shown on the color plate when a print separation is sent to a postscript
printer.
the composite from the same file prints just fine.
2.  The boxes with graphics and background dropped out show lines in the
separation plate.
I'd appreciate your help soon, I am on deadline!