I need to hard wire the Sub Outputs through the harnesss loom.
The thing is I only have three pinouts that I can sacrifice:

Pin #2 - amp. remote
Pin #12 - microphone sleeve
Pin #24 - microphone tip

I would need two for R+, and L+...
Would it be a bad idea combining the two negatives together?
(The other two sets of audio outputs have the grounds combine...)

*Ideally* you'd want the sub grounds to be exactly the same as the other output grounds - so splicing into the loom would achieve this. If you didn't do this then there might be some potential for a ground loop. However, without knowing what the sub board schematic is, I can't say for sure. I would expect that Maczool has done a good design job on the board and that the sub out ground is distinct from the digital ground but you should check.