I must admit that I don't fully understand the question, but let me see if I can help. You probably know most of the below, but I am covering all bases.
If you hade a new dedicated head unit and a new dedicated 4 channel amp with a 6 speaker system, then there is a problem. Generally, you should not run 6 speakers directly from a 4 channel amp... unless there is a crossover that takes care of 2 sets of speakers (components).
Generally if you have a dedicated amp, you will have to run;
Head unit --(low level signal)-->Amp--(speaker level)-->speakers
So if you are reusing the existing lines, your amp could theoretically replace the Nissan amp with yours and run the corresponding low level wires to your amp and the correct speaker level wires to your speakers.
In order to figure out which wires go to where, this might help some;
http://installdr.com/InstallDo...5.pdf
Unfortunately, what I don't have and you definetly need an idenftification of each color wire. For that you will have to do the search.