How to one organize SMT parts prior to/during PCB assembly

There's generally no need to do this, because when the stuffed board is run through reflow, and the solder melts, the surface tension of the solder pulls the parts into a centered position over their pads.

If the centering action of the solder surface tension doesn't give accurate enough centering for whatever it is that is motivating this idea, you have a problem. Because if you make your part-locator "stencil" with tighter tolerance than the solder will achieve on its own, then in reflow the solder will pull some of the parts against the locator and you will need to be very careful removing the locator to avoid damaging the parts.

Even with the surface tension working in your favor, some problems can still occur, like tombstoning, but this wouldn't be solved by your idea.

Edit

Re-reading your question, I see you might have another idea in mind--the stencil is used as guide for hand-placing the parts, and then removed before reflow.

In that case, why not just design your silkscreen to give adequate cues for parts placement? Then you don't have to design (and pay for) a whole extra fabricated part that will have to be built as an expensive one-off.

Have a differently shaped solder mask on pin 1.

For surface mount processors, you could have the pin 1 pad be noticably longer than the others.