I did another show at the same venue last night so got a 2nd run at this.
Made a whole bunch of adjustments based on the feedback here and got better results.
Changed the position of the mic, gave it a bit more gain than last time, and fed it to both sub and mains (with HPF set on the mains to keep from overlapping too much).
Outcome was better sounds and more presence, both for kick and floor tom.
The toms actually had a bit too much sustain (in general) for my liking. I had modified the threshold on the gates in order to minimize spillover, but I guess perhaps I need to look at release as well.
The line-out from the bass amp really sounded great through the sub, along with the low end from the keys.
There was also a conga used in part of this show (some Santana of course), so I moved one of my overheads for that, and repositioned the remaining overhead in the center of the main kit.
Only modification I needed to make on the fly was reducing the frequency of the HPF on that mic because I had set it for just capturing cymbals on the main kit.
When I switched it to the congas of course it was missing a lot of low/mid stuff, which I quickly realized and easily adjusted to bring back.
The main discovery I made this show is that the internal recording off the main signal is useful for mixing into a live room recording, but not much good on its own.
If I'd thought about it much I would have anticipated why pretty easily. Keyboards and vocals were too heavy, while guitar and bass were too low.
Guitar, because I'd set the levels in the mains lower than other instruments because they had big tube amps on stage creating additional volume vs. keys that didn't.
And bass because I had high passed the mains to keep a bunch of the bass in the sub (which obviously doesn't get recorded by the app).
Next time I'll use aux 5&6 to feed a custom, more balanced mix to the XLR inputs on my Zoom H4N and see how that goes.
Frankly I was too busy making adjustments on the fly during the show to have really paid much attention to it last night but expect with practice I could do both.
Overall, the DL1608 has been perfect for me as a novice. I didn't have any analog stuff to unlearn, and it's easy enough to experiment without feeling like I'm going to break anything.
And wandering to the middle of the house to mix from the audience is the only way I can imagine ever doing this.
Thanks again for all your help!