Dissonant chords

With progression's layers, you can only operate with two different instruments. You assign a layer to e.g. piano left hand and another to piano right hand, and you get two hands playing a dissonant chord based on the two layers.
Would be cool to have this option for single segments, but I don't think there's one, and it will probably be confusing anyway.
Having two instruments doesn't necessarily mean that you can't redirect them to the same sound, though. So for that particular measure you can just have a second track named "Piano B" or "Piano layer 2" and add some symbols there.

The other solution that you described works too, and it's probably better if you only want to obtain some specific dissonances here and there. Layers are more for Stravinsky-like polytonality compositions, where e.g. a flute plays in one tonality and a cello plays in a completely different tonality. But for simple dissonances, using the chromatic value seems more appropriate.

Not sure if you meant the "Chromatic" option for a specific symbol, or the whole "Chromatic" parameter in the "Figure" section. But both can give the wanted effect, the difference is that with the first, you change one single note or more notes individually, the other one simply transpose the whole figure.

I found that the polytonality layer system only seems to work with known chords e.g. augmented and seventh etc, and then allows to split them into simpler chords.

No idea what you mean.

the chromatic parameter in the figure section is what I used, and I set one instrument to +1 and another to +2

Yes, it all depends on what you want to obtain. A "random" dissonance or a specific polytonality effect. Or, just a single dissonant note standing out. Each of these cases require different solutions.

I didn't understand what you meant by "splitting into simple chords".
It's not much about "splitting", more like my example of a Stravinsky-like polytonality piece.
But if this

You can have up to four layers and assign different instruments/tracks to them, and pick sub chords for each layer.

is what you meant, yes, that's correct.

How do I go about getting Synfire to accept chords such as a combo of C minor and Db major? 

You can define it as a new chord type in the catalog. See picture.

And yes, the layers are not meant to be used to build up real polytonality. It works as you described.

I tried the second method, and it's a quick way to add interest and surprise to a phrase. I experimented with various Chromatic settings, Container lengths, and Container positions.