im wondering if the longest wire is powering the sub?
The longest one in that picture is powering the sub; if you look at it, it has two wires going into a single connectore, whereas the others use only one wire per connector each.
It would appear that the sub has been powered via a mono output in the past. Simplet solution is to either chop that one connector off and solder on two new ones (giving yourself a third full set of RCA's) or replace that set if you aren't comfortable with soldering.
There are options for connecting a multi RCA set up with only a single set of outputs, however, thet are very difficult to set up as the qualistation and gains are adjusted through pots on a crossover network and they will be set at fixed parameters, not easily adjustable per track/music type/vehicle passenger loads etc.
Far easier, as other have suggested, will be to trade your headunit for something with three sets of RCA outputs - typically a front set, a rear set and a non fading (sub) out.
This will allow you to connect each amplifier correctly, and give you full fading functionality from your headunit.
