Hi T Nation!
i just discovered the 5/3/1 method and i am gonna do this for quite some time.
How ever a got this question:
(lets say you are gonna do shoulder press at 1. week)
Are you then suposed to do:
thereby doing a total of 9 sets?
that would at least make sense.
And then for the following week 3 reps for a total 9 sets…
Best
Thomas, DK 
Which template are you referring to? The base program?
If you’re talking about the base program, it runs
5 reps x 65% of TM
5 reps x 75% of TM
5 reps x 85% of TM
Three sets total.
After that, you choose the work you want to do or follow one of the ten thousand templates. For example, you might use First-Set-Last and Joker Sets. It depends on your goals and what you need to achieve those goals. I don’t recall a template in which I have seen 9 sets of the primary exercise structured the way you presented it, but I haven’t seen everything Jim has put out on the internet.
In the original version you push the last set to amrap (leaving 1-2 reps in the tank). So the 3’s week could go something like this:
Warm up:
5x40%
3x50%
3x60%
Work sets:
3x70%
3x80%
7x90%
Learn about the TM, use FSL (first set last), pick 1-2 assistance exercises and you’ll be good.
I recommend you to read beyond 3/5/1 - good stuff in there.