So I have all the EM1 essentials... Like a sub-woofer.... HID fogs and headlights... heater, ac etc. So the issue seems to arise during an excessive use of electrical accessories. My idle fluctuates when sub-woofer hits hard during heavy bass songs and when it gets quiet, idle immediately stabilizes. Head lights sometimes cause idle to fluctuate up and down while parked or at a red light etc.... The moment I turn off the lights the idle stabilizes that very second. What could be the problem? I believe battery and alternator are good. I never have trouble starting the car in the mornings...

 

Test alternator

 

As with any electrical issue, grounding is almost always an issue, so start by redoing your main ground, DO NOT just eyeball them, disconnect/clean/reconnect, batt. cable clamp, batt. to chassis and chassis to engine ground.
If that does not solve the problem have the charging system checked, any batt/alt shop, [Interstate Batteries] will do that for free, it only takes a few min.

Questions...
What size amp, [make and model] do you have?
Where is amp mounted?
What gauge power and ground cable are you using for the amp?
Where is amp grounded, how long is the ground cable?
What kind and size, [amperage] fuse is on the power cable?
What is the MM&Y of the car and is it still the stock alt.?
How old s the batt. and what kind is it?
94

 

I bought the car with this issue already present, 2000 civic si. I'm going to check the details you asked for. Plus clean the main ground wires coming off the battery.