paste mask pcb
IMO Top paste should be used for solder paste, not glue. Top Glue should be used for that. But if thats how you create a glue screen then I bow to your use of it as I have never actually used glue (nasty sticky stuff!).
The paste stencil has apetures in (holes) equal or smaller than the SMT pads so that solder paste can be applied to them using a solder pasting machine (be it automatic or manual) before it is sent through the placement machines.
It is common for the pads/apetures/holes to be reduced by about 10% so that there is less solder paste on the pad, this helps to prevent solder balls etc. The amount of reduction is depentant upon the manufacturing process itself.
As for the top mask layer, this is the solder resist (green stuff) clearance around the pads. if you can assign a different sized pad to this layer you can make the clearance already without having to add it during photoplotting.
A clearance of aprox 8 thou is normal.
It is also a useful layer to add figures etc in the solder resist I.E. a strip of solder resist through the land of a non PTH mounting hole on the bottom copper can often help avoid the hole filling over during wave soldering.
For VIA's you can make the pad size zero on this layer so that they are under the masking (assuming you cannot turn them off) or in fact you can give some of them larger pads to allow them to be filled but other zero so that they are not. (filling via's is another matter altogether).
I would suggest that you have a good look into the uses of your layers, what facilities are available through them and define a standard use for each, then stcik to the same naming conventions etc. That way any macro's or batch processing will work with them all.
Oh, and have a good Christmas..
Roland.