Interesting that I had a very similar experience. A few years ago I did a Warmoth Gecko fretless 5 string build and wanted it as simple as possible. Didn't want any fancy on-board preamps, EQ, etc. I wanted just a bridge pickup and had an EMG 40TWX lying around from a previous experiment, so I spec'd just the one EMG 40 size pickup so I could try it with that and still have the option of trying something else later. It just has a single push-pull volume for the single/dual coil select and the active tone control, i.e. 2 knobs. I actually did try a single Zen Blade in it awhile later and while it sounded nice, it lost the heft that I got from the TWX being just the one bridge pickup, so the TWX went back in and stays to this day. I turned the pickup 180 degress so in single coil mode, the J blade of the pickup was closer towards the neck to keep it from sounding too thin. I would say it works well.
Now since you are going with two pickups, that may not matter as much but in either case I would have it routed for the EMG (45 size I expect) so you have the option to swap both types of pickups. You could do EMG DC or CS pickups (X or non-X), but with a pair of TWX's for instance you have a number of tone options with single coils or dual coils. You could do series / parallel / (maybe single too) with the Zen Blades as well but my experimenting with the Zen, at least in the bridge pickup, the series connection sounded best to me for that application.
Here is the bass in question. Plenty of girth, growl, and mwah in this thing.
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