I've done this so let me pitch in. Basically treat each run as if it was the only run. If you have a battery in the back fuse before each battery (so 2 fuses per run).
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MECP Certified.
Alarm: Viper 5200
HU: Stock
Active Set-Up
Tweets: Image Dyamics CD1pro mini horns
Mids: Sundown Neo Pro 8s
Amp: Kicker IX500.4 (2)
Sub Stage
Subs: (2) Dayton Audio 15" HF
Amp: Kicker IX1000.1