According to what i've red here, in the beginning it only output one channel (R or L) but a firmware release made it output both from sw output. with the y it will be double mono as in one R and one L outputting diferent sound (corresponding to each channel) or 2 channels outputting the same?
The sub out is mono, most likely a 'mixed' L+R signal, and a low-pass filter. Generally speaking, you cannot separate the L+R from this mixed signal.
If you connect that signal to two subwoofers, you'll need a "y", which is a very simple connector allowing you to run the 1 source signal to two devices (your subwoofers).
The result will be your 2 subwoofers will have the same signal - and both mono (L+R).
That's not an unusual setup. Because low frequencies are not considered 'directional' (below some reasonable frequency - maybe 80-100Hz?), you aren't losing much, if anything.
(I suspect that logic is also applied in the music mixing much of the time - but not all of the time).
But if you're subwoofers' crossover is higher - 120Hz? you may want to find an amp with a 2 independent sub outputs ( or a source with 2 sub outputs - like miniDSP, and a multichannel amp)
(Edit: I'm cringing from the possibility of debate from my casual statement: "low frequencies are not considered 'directional'... I know that all sound waves are 'directional', but our ability to identify the direction of the source at such long wavelengths is a better way to explain it. And yet, still allows plenty of room for arguments - please consider the goal was to help answer zeluxao's question!)
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