how stuff like harmony actually works

Go get a keyboard and play a chord (e.g. 1-3-5 of a scale, like C-E-G in C Major). Hold one or two of the notes in place and then shift the other(s) up or down one step in the scale -- e.g. moving two fingers from C-E-G to C-F-A gives you the I-IV chord progression. (C-F-A is an inverted chord, but it's still a IV functionally.) You can also shift all the notes up/down a step -- being mindful that the diminished chord vii° can sound off. (You can think of it as a V7 missing its root though. i.e. B-D-F vs G-B-D-F in C Major.) You can also jump from I to anywhere or anywhere to I if you want. Some of the progressions you can make with these patterns are very strong like IV-V; others are weak like IV-iii, but if you just play with it, you'll get a sense of what works pretty quickly, I think. The basic idea gets you most of the popular simple chord progressions like I-IV-V-I, I-ii-V-I, etc. anyway. Adding 7ths gives more color, and V7 (the dominant 7th chord) is a particularly strong one -- it really wants to resolve to I (which you can either allow or subvert when writing music). There are also things you can do with half-steps and borrowed chords when you want to get more creative, sus chords, etc. but thinking about how the fingers move on a keyboard is what made things click for me when I was learning this stuff ~20 years ago. (I think you can have a similar sort of realization via guitar, but I never really got into guitar, so I think in terms of keyboard; I'll defer to other's experience if you prefer guitar over keyboard.)

If you aren't experimenting with an instrument capable of chords, get off YouTube and go play an instrument for a bit -- you will learn more (and more quickly) by just pressing the keys, watching where your fingers go while following the patterns, and listening to how it sounds than you will get from hours of theory without mechanical experience.

chords?

totally depends on what your ultimate goal is.

independent from that, i recommend the highly customizable exercises at musictheory.net - knowing how stuff works is good, practicing it until you recognize it instantly in sheet music and/or on the keyboard is a whole other beast.

I vaguely remember seeing a really good interactive tutorial that dealt with most of the music theory. It must've come heavilly recommended, because that's what I usually search for when learning stuff.

It was years, though, I'll see if I can find it.

But I'd go with scales or chords, depending on what you're playing.