how does rune upgrading work in diablo 2 resurrected?

Low runes are just 3 of the same in the cube = the next rune up. That works from El all the way to Ort into Thul. From Thul up you add a gem: 3 Thul + chipped topaz = Amn, 3 Amn + chipped amethyst = Sol, and so on. The gem type cycles through topaz, amethyst, sapphire, ruby, emerald, diamond, and each time round the grade goes up, chipped then flawed then normal. From Pul upwards it's 2 runes + gem instead of 3. Don't cube your low ones too soon though, the cheap runes are what you need for early runewords like Stealth and Insight.