As he said, the only way to really figure this stuff out is to start tinkering. The good news is you can begin to do that right now, although there is a limit to how much you can learn without actual hardware and licenses.
in fact, I just went over a lot of this kind of stuff with another newbie that just joined. So I'll copy/paste almost verbatim the stuff I emailed to him just yesterday. Here you go...
Binary Editor can be downloaded & installed for free. But in order to use it for writing tunes and datalogging, it must be registered. When paying your registration, you have to send in a registration code. The code is a combination of your licensing user name and what devices you want to use with BE. For the base price, you get one major tuning device (e.g. the QH), and one minor tuning device (e.g. an Innovate Wideband). For those that want to tune with more stuff, the price goes up. For now, it will do you some good just to get it installed, opened up, and displaying tune info so you can begin getting familiar with the various settings. When talking with people on the forum about GUFx parameters, you'll often want to use the PID names for things like FN1360 or Z_AFR. Those will be more descriptive as to exactly which setting it is you are talking about.
Now is also a good time for you to read over the FAQs on the tuning forum and learn about things like exactly what scaling functions are. Understanding them is pretty foundational to tuning and you can start messing with scaling functions with BE unregistered.
A QH holds up to 8 modified tunes, each that can be flipped to on the fly while driving. That sounds interesting, but unless you are running a NOS system or setting up a tune to run regular, premium, and E85, the main thing the multiple tunes will be useful for early on in tuning is to have a "safe" tune, an experimental tune, and maybe a valet tune which is a tune that won't let the engine run over about 5MPH or over 1500RPMs. You could setup an all-out anti-theft tune which won't let the engine crank & run.
So yes, BE is the software you use to modify the tune with. BE is also the tool that lets you configure what you will datalog and will do the datalogging of the QH. The info from the QH will be displayed in real-time on the dashboards as well as saved in datalog files.
EEC Analyzer is the software that analyzes those datalogs. Strictly speaking, you don't need EA to tune and in fact some of the experts here don't use it. Practically speaking, EA is worth every penny to a newbie to help you view the mass amount of data in more logical ways. EA is used to help you dial in your MAF curve and Injector Slope/Breakpoint values. EA also has charting and mapping features which are great for looking at other aspects of your datalogs. There's a number of other tools in there, but most of the others are not as useful as they look. The one everybody obsesses over is the Injector Timing tab since that's where you enter Cam info. It looks impressive, but it really doesn't do much. Injector timing is the least significant part of the tuning. It's fine tuning, not roughing in a tune which is where you'll be for a number of weeks in the early days. Put another way, the engine cares far more about getting the correct amount of fuel than it does about the exact time the fuel is delivered relative to the intake valve. So because of this, injector timing is just not that important. FAR FAR more things to obsess over. EA is only used for analyzing your logs. While it was used to datalog EEC-V many years ago, since then, BE has taken over those responsibilities. The capabilities stay in there just because it's already there so why not leave it? None of that stuff will interest you. The main things you will use EA for is MAF curve tuning, Injector Slope/BP tuning, and using the Chart & Mapping features. That's 95% of EA's value...the rest is just stuff to play with basically.
Anything else I could say would just be a repeat of things that are already covered in the FAQs.
89 Ranger Supercab, 331 w/GT40p heads, ported Explorer lower, Crane Powermax 2020 cam, 1.6RRs, FMS Explorer (GT40p) headers, Slot Style MAF, aftermarket T5 'Z-Spec', 8.8" rear w/3.27s, Powertrax Locker, Innovate LC-1, GUFB, Moates QuarterHorse tuned using BE&EA