My question comes from seeing the instructions for the delta fan controller. It shows wiring the fan controller directly to the positive and negative battery terminal. In this configuration, how will the higher amp alternator be powering the fan during normal use?
The battery powers all in your electrical system. The alternator just keeps the battery charged as needed. It does not matter if you hook directly to the alternator, the battery or through the fuse box. There is only one electical system. 12v is 12v. ground is ground.
The delta fan controller you wire directly to the battery because it's a high draw item. Same as the starter and how you'd wire a winch too. The controller has short protection built into itself so there is no fuse, fusible link or circuit breaker in it's power wires.
BTW, you won't need anywhere near 200 amps. Your 50 amp alt will probably keep up with the demand fine most of the time. In normal use, the fan's only gonna draw maybe 10 to 15 amps, and probably nothing at higher speeds. Maybe if you're over-heating so the fan's at full power, at night with the lights on, stereo blasting, in the rain with wipers going, etc. That's one of the nicer things about the controller, it only sends enough power to the fan to keep the motor cool. With the full shroud and double row radiator, I wouldn't expect it to need full power very often.
I think upgrading the alt is a good idea (50a is a bit small), but realize the alt will only put out the amps that the vehicle is drawing. When you exceed the alt's limit, the battery fills the gap, then charges back up when the load drops below the alt's max output.
If I were to add other accessories could I simply come off of the positive battery terminal as well? Would the alternator power the items "through" the battery somehow?
Yes, but I'm not a real fan of running a bunch of wires directly to the battery. It gets messy and confusing as heck after 6 months and you don't remember what wire is what. It's much cleaner to get an aux fuse block. Run that to the battery through a fusible link, then hook your accessories to the fuses in that. If you go with junkyard parts, you can find small blocks with fuses and relays as well for higher loads. Draw a diagram of your fuse block and update it with what fuse goes to what as you add stuff and it makes it easier for future maintenance.
I was thinking that I would need to slip into the existing wiring to set these types of things up?
This is only a suggestion. I've wired in an aux fuse/relay block from a junkyard (TJ I think. this block is nice because even though it's big, it's filled with small removable sections for fuses, relays or fuse/relay combo that you can pull out rather than use the whole thing). I've got power to it from the battery, and also a power wire that comes on with the ignition, and another that comes on with the charge relay so it's powered only when the engine is running.
When I need to add an accessory, I can use an empty fuse and/or relay to power it either all the time, with the ignition or the charge relay depending on which power wire I use to trip the relay.
--Dan