The best means is what handrawn points to. If all you want is a single color, the convert to duotone dialog loads with only a black ink. It begins with a single ink in monotone mode. That color is a Pantone Black by default. Double click on it to change it to another Pantone. If you want to add more than one ink, change to duotone, tritone, quadtone. Make sure to adjust the curves.

A truly simple, yet not as precise means to change the color on a gray image is to simply use the Hue/Saturation. Play with it a bit and you'll see the effects.

As for output, unless it is destined for spot color printing, it will need exported as an RGB or CMYK image format.

As to transparency, you can use the cutout lab. Generally works well.