What kind of batteries do you have and what's the weather like where you're at? Sometimes when you add a second battery, if it's in the trunk and the weather is cold, this may cause excess load on your alternator. This can also happen if your batteries are not matched, one may be losing charge quicker than the other, then your alt has to work overtime to get it charged up.
Also, this may be normal, you may not have noticed it in the past because of the fact that the Big 3 wasn't done so you may not have been getting accurate readings..
Check this out.
I decided to run a Fosgate T30001BD on a pair of JL12W7s.. I came across the Fosgate amp on Craigslist, picked it up for $300 BNIB. Some poor idiot bought it "WITHOUT HIS WIFES PERMISSION" (that shit cracks me up, grow a pair, anyway, his loss, my gain)
Until then, I was just running 4 Gage from the main battery to the Optima in the trunk, Mmats D3500.1 for subs.. Mind you, I had just installed the JLs about a month before, didn't have much time to do anything, just slapped it all in there rush job.
For music it was fine, the bass hit pretty hard but I knew there was much more in it.
When I came across the Fosgate, I couldn't pass it up, I knew that if I didn't like the amp, I could just as easily sell it and double my money so I pulled the trigger.
I hooked the amp up and noticed a big drop in output power, lights dimming badly, distorted sound.. I hooked a MM to the main battery got a reading of 11.8 (all this is just going from memory) At the alternator, I was getting almost 14 volts, at the Optima I was getting 11 and change, even lower than the main battery, when I used the chassis ground under the hood, I was getting an even worse reading.. The point is, I was getting ridiculous readings everywhere. Bad grounds, faulty wiring (98 Acura CL, Northern car, lots of rust)
I decided to get the Big 3 done. (put it off because I didn't have time and the Mmats amp was OK the way it was)
I removed all of the factory wiring from the alternator all the way to the main fuse box under the hood. I put nice 4 Gage from the main battery to the chassis and engine, put an extra 4 Gage from the engine to the chassis. Then I went 4 Gage from the + of the main battery to the fusebox under the hood. Went 4 Gage from the + out from the alt to the + of the main battery. Went 0 gage from the main battery to the Optima. Grounded the Optima to the trunk floor with 0 Gage. Then grounded the big digital cap to the trunk floor with 0 Gage. Ran 0 Gage to the Fosgate from the trunk floor, 0 Gage + from the optima to the cap, then to the Fosgate. After all the wiring was done, I put the MM on and got a reading from 13.4 to 13.6 anywhere I put the MM to.. This did the trick.
When I tuned the amp and put in Bass Mekanik, I couldn't believe my ears.. 30HZ and lower on the test tones from the Bass Mekanik CD were the only thing that made my lights slightly dim, that's with the Fosgate amp. (Fosgate is a serious current hog)
I took the Fosgate out, installed the Mmats D3500.1, it hit almost as hard as the Fosgate, but it never made my lights dim. I ended up blowing 1 of the surrounds clean off the cone with the same 30HZ test tone, destroyed one of my JLs.. This is despite the fact that the Mmats amp wasn't delivering its full payload, it is designed to do 2700 watts rms @ 1 ohm, the JLs were showing it almost a 2 ohm load which I was told was robbing me of nearly half its power..
I sold the Fosgate T30001BD for $750, now I am selling the Mmats D3500.1 and the 2 Matching Mmats 4 channels (SQ4150 and SQ4160)
Looking for PPI Art series amps, beat up for cheap if possible, the cheaper the better, don't care what they look like as long as they are functioning 100% and are all original inside.. Need an A600.2 and an A300.2 or an A404.2.
Anyone with beat up .2 Art series amps please send me a PM. The cheaper the better, prefer beat up amps because I am going to refinish them with custom powdercoat and graphics..
Anyway, back on the subject, you may have nothing to worry about. As long the voltage jumps when you rev, you should be alright. The only other thing I can think of is that you might want to check the voltage at the alternator when the car is idling, put a MM to the alt and chassis and check your voltage right from there. If you are getting a different reading at idle (different from your digital display) then pull the grounds off both batteries and check the voltage from each. If one is down on power, go back through your wiring. (But before you do that, make sure to pull the grounds and check both batteries.)
If it's not your wiring, and if your batteries are off, you may want to consider matching batteries. If one or both of your batteries is not up to snuff, it/they may be putting a heavy load on your alt, that is in addition to the current draw from your amps.. This will lead to bigger problems later..
Summary:
A) Check Alternator at idle. Use the Positive and Negative directly from Alternator for the first reading, if it's the same there at idle (same as the reading you're getting with your voltmeter) then it's the alt or regulator. If you are getting a different reading at the alt then go to step B
B) pull the grounds off both the batteries (with the car off) check voltage on both batteries. If one is off, then try a pair of matching batteries. Use Gelcaps front and back. If they are both good, then go to step C
C) Go back through your wiring, put a MM everywhere, find the bad connection or ground. Make sure that all of your grounds are as short as possible, put as many grounds from the main battery to the engine and chassis, alt to chassis, trunk battery to trunk floor, make sure all of your connections are solid, when grounding, make sure you grind till you have lots of bare metal, then use the special battery grease to keep it all from rusting..
Hope this info helped. Good Luck.