The rendering engine had a minor bug in it that I fixed tonight (You may have placed your order while I was editing the code, which would have created unusual pad layouts). The stencil will be fine, the render engine is there to give you an idea of what your stencil will look like and to give you a better idea of border visualization to save costs. (ie: shrink/increase your border as needed). The pads should line up flawlessly now.
Sometimes however the pad layout will render awkwardly, this is caused by two things. 1) The Gerber image handler (which is one of the only things on the site I didn't write myself) treats macros in an unusual manner if they don't follow the strict RS-274X format and 2) The resolution of the image is shrunk down significantly before displaying it and sometimes when that occurs really thin lines may disappear.
Your stencils are always cut using your original file however. They are then QA'd against a printed copy of your raw upload. Every stencil is lined up on the print out before it's packaged and shipped to ensure nothing is missing and that the pads are visible clearly.
As for multiple stencils, there is no quantity function (this is by design), if you want multiple of the same stencil just add it to your cart again before checkout. This is sort of a safety net that tells me "Yes, I really do want two of these". Most people never have a need for more than 1 for a small run or proto scenario.
I have had users who are doing 100+ boards order multiples but mostly because they setup a small bench with multiple people doing it thus the need for multiple stencils.
I'll make a note on the site so it's more clear that if you want more than one copy of the stencil to just pop it in your cart multiple times.
User generated text input for engraving is coming later this week. I'm almost done with that code, so you'll be able to put up to 3 lines of text via the website along one border of your stencil so you can identify it easily. This is useful for naming stencils by project, board revision, date, etc.
Thanks for the great feedback guys
I appreciate your support.
-B