Always design your stencil to the IPC-7351 standard, which is 1:1 stencil artwork, you design the stencil at the same time you design the board.
It is just a artwork that shows where the appertures are to be to deposit solder paste for the reflow of components, mainly surface mount devices, but also increasingly some through hole components such as connectors, it should also have fiducials on the artwork so these can be half etched into the screen for the printer to locate and cater for any misaligment of the screen in the printer.
The reason why you shpould use a 1:1 for the generic artwork is so your stencil manufacturer can compensate for stencil thickness and other parameters, especially if you use multi level stencils.
Stencils are probably the most critical component in the reflow line, where incorrect use, design, cleaning, squegee pressure or a whole host of other problems. So I would strongly recomend that you create an IPC-7351 standard artwork (all pads 1:1 , fiducials on the artwork) and work with your assembly department and screen manufacturer to alter the appertures to cater for you processes and component sizes used.
Have a look around this site:
Tecan - SMT Stencil Products
A selection of info from the web:
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Printed Circuit Design and Fab and Circuits Assembly October 2010
PCDFCA September 2011
Note the stencil is for printing solder paste...it is not related to selective soldering.