It’s not what you’re after but just study them outside HH since HH just doesn’t handle them at all. Personally although I initially hated it (especially the 还 as huán vs hái?), I honestly found it wasn’t that big a deal. HH won’t teach you to read or to talk - you need to do those activities yourself. When doing those activities, I found you’ll learn all the other pronunciations/uses of characters basically automatically.
Same with the other meanings - lots of characters also have multiple meanings, some of which have nothing to do with the HH key word. You just have to actually use the language and it’ll sort itself out.