Solder paste files

I have gerber files that I'm sending to a PCB house and a stencil maker to get manufactured. I use the solder paste file to indicate 1) which components should be plated by the PCB house and which should be left as bare copper and 2) the size of the aperture for the stencil.

These 2 things are not always the same - do most people maintain 2 separate paste files in this case? Or should I be using a different gerber extension?

The 2 cases we have are:
1) Hand placed surface mount components which have plated pads, but no paste.
2) Reduced size paste apertures for a QFP package, but we want the plating to cover the entire pad.

Thanks!

We generally put in the paste mask for all parts, and cut the gerber file with all of them on it. For boards we build in house (prototype runs), our techs take our paste file and modify as needed, then use the laser cutter to make their own paste stencils. For boards being assembled out of house, we supply the full paste mask gerber file, and they make their own stencil based on the assembly variant given to build.