For spells like the Hexblood's Hex Magic, where you can cast it once per long rest, and then cast it using spell slots.. How do you make that with the homebrew tools?

Other examples of this would be Fey Touched/Shadow Touched feats.

So far I've managed to make a spell lists but once they use the single use, that's it. Can't make them use the spell slots after.

You cannot with a feat, only with subclasses & races. That’s part of why the official feats only add the spell once and rely on players to simply tick off the spell slot manually whenever the spell is cast with a slot.

To do it with subclasses & races, you would add the spell a second time with no limited use data and select “Yes” in the dropdown labeled “Consumes Spell Slot.”

Gift of the metallic dragon adds a 1st level "use" of cure wounds to my sheet and also adds a "cast" feature to each level spell slots without it requiring my spell list or preparation. Is this not duplicatable for homebrew magic items yet?

No, feats & magic items cannot do that.