First, I found a good informative dual battery tutorial. I even learned something. I may need a few more cable runs than I thought
Dual battery wiring tutorial (and why)
Here's another good all around car audio reference site hosted by an electrical engineer.
Good new and bad. The good is your alt choice is very good. Singer is in my the top 4
. The HU & Infinity's are good too.
The ok....Here's your amp manual for your amp choice. Your choice
Although your amp is an ok entry level amp. But you may want to rethink the amp. It has 60 amp fuse so you really didn't have to upgrade your alt or buy any batteries for this amp. A stock electrical system with a big 3/4 in 0/1 gauge properly done can do the job just fine. To actually need 2 audio batteries you would need a 1 ohm stable type amp that actually pulls 2k watts RMS /166 amps draw or more. An amplifier of this caliber would probably have a 200 amp fuse rating.
If you have reservations about your amp perhaps a Hifonics or Audiopipe capable of 2k @ 1ohm and that shouldn't break the piggy bank.
Bottom line is that your amp choice and subs WILL bang [in the right box]. I stopped messing with boxes in 1995 and don't give advice on them. Your system will bang but the battery plan is overkill for a sub amplifier that is only fused at 60 amps. It's like putting 108 octane gas in your 87 vulcan powered bull. You'll be lucky to pull maybe 40-50 amps tops from your Sub amplifier maybe. Your electrical with the alt upgrade and 0/1 is ready for a 160+ amp RMS draw with the Singer Alt. So you are running practically 100 extra amps surplus of current. With that alt your going to be slamming & flexing.
You can use that battery money to get soundproofing in your trunk, rear deck, spoiler & license plate. I would wait and see how your system performs first, then ONLY if your lights dimm. Only then I would get the batteries. But I bet your lights won't dimm. The alternative is to wait and save and get the next level stuff. Perhaps a sundown 1500D or a RF1500bdcp and some corresponding subs to compliment the amp.
For starter systems I like the Kicker 12" Sub Competition line best because for the money they are "the stuff". *cough*. But your Boss sub firing forward into the cab should get the job done. The Boss sub you picked out received some good reviews.
Yes the a heat gun will work for the heatshrink. HF sells them cheap.
I have my primary D31 battery under the hood & my 2nd D31 battery in a battery box in the trunk hugging the fender well like everybody else. We all need access to our spare tires. This is a picture before I installed the 2nd Blue under the hood.