I use the single element pickup with a 2.2nf capacitor in the output jack. That’s what I would recommend based solely on my experience. I’ve never tried the two element pickup up. One thing you could do if you wanted is order 2 elements, try it with both elements and single. It’s easy to do that simply by disconnecting the short cable between the elements.
A slight tangent about the output of the Yamahiko. I personally found this pickup almost unusually with the stock output jack, due to high enough output to distort my Clarus and my WW, with or without the fishman preamp I have. I tried soldering a capacitor in a spare 14” cable, and that fixed the problem. There are a few threads about this on this forum, lots of good info. Once I found the right cap value (for me, 2.2) I ordered an output jack (he calls it the output cable) from yamahiko and now I can use any 1/4” cable.
Ok, so that got me thinking, why is such a well built and well thought-out pickup delivered with such a high output to distort on the low E, even with high quality amps? Recently, one of the more knowledgeable posters on this site (maybe doublemidi) posted something about how the 2 element design results in a drop of output voltage. That makes sense; maybe the standard output is optimized for the 2 element model. I’m guessing here.