Steven, the Atomic is designed to work with the POD, so the poweramp is pretty neutral and shouldn't colour the tone, it also uses the POD as the pre-amp as far as I am aware, thus allowing for all the POD tones to be reproduced faithfully. I wanted to try one of these when I found my POD less than satisfactory through a valve amp, but no one had one near me. I'm glad you found it sounded good, maybe I should revisit and see if I can try one, but having just started a OT kit build I think I'm going to stick with all valve now!
Now your problem will come when you use the POD in front of the OT. The OT has a character of its own and I doubt whether you will find it satisfactory used in conjuntion with the POD, but you can try it. I doubt you'll find it satisfactory in front of any valve amp, and you'd be better plugging straight into the PA with it. This is my backup plan for if my amp goes down, it does work and a lot better than through an amp IMO.
You can also try it straight into the Poweramp In (FX return) which was how I used the POD with my HotRod. You will always lose something whichever way you do it, thats why I suggested an A/B switch to take the POD completely out of circuit.
Well, power amps, by their very natural and design, are all neutral. Voicing comes from preamps, power amps just...make bigger. That's not to say they don't have their own behavior, that's why we like the crank Marshalls.
But I agree that everyones mileage will vary when matching POD and amp.
eriwebnerr have the correct setup for how to connect.
What also has to be done is setting the amp bypass mode, there are 4...COMBO FRONT, STACK FRONT, COMBO PWRAMP, and STACK PWRAMP...I think it's self-explanatory which is used for which. The manual goes into more detail. And want to turn the speaker sims and AIR off.
What the OP needs to decide is what effect they will be using and how. Very few pro and long-time players use reverb with distortion, only with clean to low gain tones. So, will you need or want reverb after the preamp? Maybe, maybe not. In really dead rooms, a little slapback delay can be used, which works just as well in front of the amp as in the loop.
Long delays would probably sound best in the loop, as would chorus and phase is used with heavy OD. But compression may be too noisy there.
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