One transfer switch, two main panels
OK, so a) you have 400A class service, or some other good reason to have dual main panels with dual main breakers.  And, you are ready to install a fairly large electrical box right next to them. And c) you are OK routing wires or cables from both main panels to this new third box.  Those are all the ingredients we need to succeed.
But send it back. It's the wrong thing.
And way overpriced and very limiting, compared to what we're about to do.
Honestly, it's usually the wrong thing, because the inherent design of those boxes was a 1970s-tier &quot;hack&quot;. Generator salesmen love 'em because they feel like they're sending you home with something &quot;that'll work on any panel&quot; - but they are thinking of obsolescent panels like Zinsco or Pushmatic, where there is simply not an option for a proper full-panel interlock.
Today, the problem is this old hack doesn't play well with modern panels, like your dual panels, AFCI, GFCI, power monitoring, or any of the neat stuff Leviton is doing with their smart panels.  In fact they cannot provide AFCI protection and don't provide GFCI either (unless the generator does, but who wants the entire house tripping out)? If AFCI/GFCI is mandatory, it's mandatory in generator mode too.
Either of the methods below will take care for those problems, and happen for around $100 give or take - certainly not $500.
Option 1: Get a full-panel interlock for one panel ($60-100)
based on your photo on DIYchatroom, you'd need to retrofit main breakers ($100) into these panels to implement this option. However, this would be the easiest thing to do, and these quite-new panels definitely have interlocks available for them.
Normally, when you have dual main panels, it's because of 300+ amp service that is simply too big to economically do on one panel.  That is fine as long as the panels are next to each other. (main disconnects must all be in one place).
However, the usual way to set up dual panels is to put your BIG loads (on-demand water heater, or the #1 application, heat pump emergency heat) into one of the panels -- and all your normal residential loads (receps, lights, etc.) in the other panel.  Typically these loads are far too big to ever be able to power from a generator, it doesn't make sense to do that.  So you &quot;write off&quot; the big-load panel.
So that makes generator layout very simple: you only need to support one panel.  Put the usual whole-panel generator interlock into that panel, and you're all set.
If your loads are scattered all over both panels, my advice is to correct that.  If it's possible to simply re-route the Romex cable, that's great.  However, if not, you can use the &quot;old&quot; panel as a splice box, and carry over hot and neutral to the new panel. You must bring over both the hot and the neutral as a pair. You cannot leave neutral in the old panel; it MUST come over to the new panel.  However, you can leave safety ground in the old panel.   Neutral is not ground.
If you need to do several circuits, the best way to do this is with one or several conduit runs between the panels. It's possible to install acceptable conduits without removing a panel from the wall.
Option 2: New subpanel with generator interlock. ($90-120)
Like we say around here, &quot;Think BIG&quot; about panel size.  A modest 24-space panel will switch 20 AFCI circuits or 40 plain ones between utility and generator. The problem, as you know, is you don't use many loads at once but they are scattered on many circuits. By using a whole panel as an interlock, you can support a large number of circuits.
We recommend spending a few lattés on a size bump to 30 or even 40 spaces.  Nobody ever came on here saying &quot;I want to add a circuit but I left myself plenty of spaces, what do I do?&quot;  But the line is around the block of people who chintzed out on panel size and regret it.
You get a panel either with a main breaker and factory-made generator interlock kit, main-lug/no-lug and you fit two 2-pole breakers with an interlock between them.  These are are back-fed, one by utility and one from the generator inlet (which can be anywhere you please; in-wall UF cable is cheaper than heavy generator cord and a darn sight more convenient.)
At that point, you move any circuits you want on generator out of your regular panel into the new panel - as said above, using conduit if able, and both hot and neutral wires must come over together.
If any of the &quot;to be brought over&quot; circuits are on AFCI or GFCI breakers, take close note of the make of the breakers.  Choose your gen subpanel so the existing breakers are legal in it (generally, don't cross brands; they will seem to fit but will burn up the bus bars).  That way you can just move your valuable breakers to the new panel and save $40-60 each.
On regular breakers I'm not so worried, they're typically $5-ish.
Yeah, but you really, really want to save that panel
--Why?  They ripped you off. And it won't even function with your AFCI breakers, and problems like that will just keep biting you: it'll be the path of pain. Don't fall victim to inertia or &quot;the fallacy of sunk costs&quot; Even if you can't return it, unused/complete transfer switches sell pretty well on eBay/Craigslist. It will fetch a fair bit more than the above solutions cost: you'll be cash ahead!
But OK.
The transfer switch can only serve circuits in one panel.   Reliance tech support can't &quot;waive&quot; this requirement; it's in NEC 110.3(B).  When UL approves equipment like this, they also approve the instructions and labeling. UL only approved the device for uses according to the instructions and labeling; they didn't even test it otherwise. The companion law is 110.3(B) which says you must obey those (approved) instructions and labeling.  The switch is only approved to support 1 panel, and that's the end of the discussion.
So, you need to choose 1 panel, and move circuits from the other panel to it.  That is a straightforward matter, and I discuss it at length in option 1.
It's OK to have wire-nut splices inside a service panel, and it's OK to use a panel as a splice box for unrelated circuits. So you can lift a circuit off its breaker and neutral, and extend its hot(s) and neutral together to the other panel.
In the other panel, the neutral lands on that neutral bar, and the hot(s) go to their new breaker there.   Yes, it matters to move the neutral wire.  That's what all this is about.
The hot(s) and neutral for a given circuit must be in the same cable (back to 300.3 again).
With cables, I would just run them the 3 inches straight across, I wouldn't bother going out the top or bottom.
When I have panels side by side (and I do), I like to include conduit &quot;tunnels&quot; between the 2 panels; several of them in fact.  However, the hot(s) and neutral for any given circuit must go through the same tunnel.    If a cable has enough wire length to make it through a conduit tunnel to the other panel, go for it.