You need to ask whomever's printing the document what they require. But many printers use the PDF-X1a standard because of the way it handles color and raster and vector images as well.
Sounds like you have 2 Pantone colors, not one. You might want to "Preflight" your layout from InDesign first and see if you have any extra Pantones in there you don't want. As it is, CMYK printing + 1 Pantone sounds a little bit excessive unless it's a corporate client who absolutely has to have their corporate color print correctly.
Why would you set CMYK to transparent? If you have CMYK in your doc, that's what's going to print, and the printer will have to use their 5 or 6 color press for your job. More $$$, obviously.
To export 2 colors, you can export just those colors, but the easiest way to do that is to first DESIGN it that way. Only include the two colors you want in your design. If you start taking colors out, when more exist in your doc, you are going to have color issues; like having them not print correctly, for example.
Are you printing duotone? Then set any raster images in duotone and use the pantone as the color, black as the other color. Then your text can only be that pantone or black when you go to set up your layout/InDesign file. Viola—2 color printing.
Hope this helps!