I want to run dual batteries, because, for starters, I run offroad lights, but also because when I use a power window if seems to dim my headlights a little.
Is the engine running when this happens?
When other people set up dual batteries, do they run them inline, or just as 2 seperate batteries?
The best setup for dual batteries is to have them separated with an isolation relay. In that configuration, you power the things that you want to run when the engine is not running from the isolated second battery and when it is running the two are connected in parallel for charging purposes. This makes sure you will not have a case where you run the battery down when the engine is off and don't have a way to start the engine.
If your not running stuff with the engine off, then you don't really need a second battery.
What you need is a larger alternator that can handle the load. In normal operation, once the engine is running the alternator should be supplying the load. If it can't then you will be draining the battery.
You shouldn't be compensating by adding a battery that only delays the problem, it doesn't solve it.
And can a stock electrical system handle twice the power safely?
The ability of the existing wire to handle loads is based on the demand on a circuit. Older vehicles were not wired for all the extras. In fact you can probably double the brightness of your head lights just by rewiring with heavier wire, most people do the headlight wiring upgrade to accomplish this. So can you add stuff? YES. Just make sure the wire it is connected to is large enough for the application.
For example your 100 watt lights require a little over 8 amps to run them. They should not be attached to the head light circuit or any other circuit. If you overload a circuit, one of two things will happen the wire will heat up and cause a fire or if you are fortunate, it will just blow a fuse. If you are on the edge of the wires tolerance and hooked up with some other stuff, you may see dimming, that means there is an excessive voltage drop caused by the amount of current being drawn. Solution: reduce the load on that circuit.
Note: Dimming can also be caused by poor grounding.
And is there a way to squeeze 2 fullsize batteries in the space of a single one, or do I need to look for a dual battery kit?
I have seen the second battery mounted on the wheel well just behind the first one. If I were to add a second battery, I'd put it in back with my other one. I am using the original battery location for my Under Hood Fuse Box (it replaces fused links and gives me a place to add circuits for powering my Head lights, Fan control, DRLs, Fog lights, MSD ignition, etc.
Hope that helps
This is how Ford hooks up the auxiliary battery
Good luck,

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