Don't think that you need to merge anything or something. First of all, work with CMYK then just make sure your 1 color ir realy 1 "color". Only cyan or magenta or yellow. Not like 1 color is green, because green contains (separates) at least 2 cmyk colors. If you need green (choose it from any panthone color and remember) even then use 1 'color chanell' and when you give to press say to men what real panthone color you substitute your 1 'color chanell'.
So...work in CMYK (not RGB), use one 'color chanell'. Bevel and Emboss and Drop Shadow wont produce new colors. Image will stay in 2 colors - one yours choosen and black.