How do you connect one generator to two separate boxes?
From whence are they fed? Where will you put your interlock?

I happen to have a superficially (since I know no details of yours, yet) similar setup - mine is fed from one meter that feeds both panels. I dread to think what it would cost to put a transfer switch on that feed line, so each panel has an interlock and generator input. My reasoning is that I want to be able to power any circuit without any unsafe power outage creative wiring, but not all at the same time (that would be a BIG generator and the cost of that is also outrageous.) 

Most of the time only one panel (in my setup) will need a generator attached to it, but the input is there on the other panel in case I wanted to power one of its circuits in the event of an outage - to avoid unsafe power outage creative wiring. Unless I got crazy and got two generators, I'd expect to power down the one panel and move the generator cord to the other one, rather than trying to power things on both panels at the same time. The "primary" panel in that sense is the one with the well pump and most lighting circuits on it. Refrigeration will also end up there, by design. Load control is by hand, but it's much nicer to be able to have well water (and turn the fridge and some lights off while getting it) than to haul water in a bucket from a stream.

I'm dubious about trying to feed from one generator into both panels at the same time, but if you have a large enough generator (and enough output breakers switched off) and sufficient hardware it should be possible, it's just not something that I personally looked into in any detail, as I had the thought in mind that I'd land loads I might want on a generator mostly on the one panel, but spend the small amount on an interlock for the other panel as well. I don't know if you'd have to have a sub-panel from the generator input to split to the interlock inputs, or if you could just depend on the generator output breaker at one end and each interlock breaker at the other end, with no more hardware needed in-between. Given how interlocks work, I can't see any unsafe condition arising from two interlocks on the two panels (i.e. you don't appear to be asking about "backfeeding from a sub-panel" which you cannot do.)

Depending what your reasoning (and scale of generator) is, you could possibly move circuits you expect to need to power from a generator all to one panel.