Hi Stryker -
An earlier poster was correct - due to the situation(s) with S-scale, you are probably going to have to learn a bit more than most of us about electrical control.
You really have three possible control systems: 1) AC; 2) DC; 3) DCC.
I believe that AC will only run the older American Flyer equipment, but I could be mistaken.
There are many discussions / tutorials about DC vs DCC - you have found at least one.
One thing to be very, very careful about. DCC advertises itself as being ‘compatible’ with DC. While this may be true in some cases, it is not true in a practical sense. In fact, some DCC equipment (older Soundtraxx sound decoders) will BURN UP on DC power (I have letters from the manufacturer stating this).
Further, it is very chancy to set up a layout with part-dc, part-dcc, and expect not to smoke decoders. You hear tales about this happening when a locomotive bridges a gap between sections - very frequently.
It can be avoided, but is best avoided by ditching the whole idea. For safety, stay with DC power packs or DCC power only.
This does not mean you cannot start out with DC locos, and a DC power pack, and learn. You can even - theoretically - run these ‘DC’ locos on address ‘0’ with a DCC power system - until they burn out, that is. The DC locos so run also make an objectionable ‘buzzing’ sound when run by a DCC power system - before they burn out, that is.
If you are at all electronics-savvy, I would go with DCC from the start. If bits and bytes and volts and amps make your eyes glassy, then you might want to start with a simple DC pack and one or two engines, meanwhile trying to learn about DCC. You will (probably) eventually want to go DCC at some time - but not everybody does, either.
Just be very, very wary of claims that DC and DCC can run ‘together’ on the same layout. You would be inviting costly trouble to try that.
jrc