If you are going aftermarket speakers and amplifier you will need a DSP for summing all the channels bit if you want just a flat signal with no bass roll off you can hondahack your headunit and install Viper4Android
you can go to a harbor freight or something and buy a multimeter, they cheap
Oscilloscope would be best so you know when you are clipping and if your signal is clean
also you may want to set you cross overs too
Maybe you should of gone with a dual 4 ohm sub (wire to 2ohm)or single 2 ohm sub so you can get more bass, cause I think your speakers might over power your subs
Do you have an oscilloscope or multi meter to tune the gains for the amp?
What amp are you trying to install? if its just a subwoofer amp you can use you a line out converter and tap the rear speakers but if you are installing a multichannel amp you need to tap the source from behind the head unit with some line out converter
this happened to me once when i installed new speakers on my civic, it was because of a loose connection on one of the speakers, sometimes hitting the speaker area would get the speaker going again but i just rechecked the connections and it worked
Our stock head units have Bass Roll off so after a certain point the bass does not increase when the volume does, setting gains wont really help and yes an AudioControl LC2i with ACCUBASS will help.
Do you have the 7 inche touch screen? if so you can get hondahack and get android viper4android...
I used this tool
And your DSP might have a phase function so you can just correct it there if some speakers are not on the same phase