It's pretty easy. You can opt into any ligature you like across every mode, and then add extra ones for each programming mode or other mode. For example:
(use-package ligature
:ensure t
:config
;; Enable specific ligatures globally across all modes:
(ligature-set-ligatures 't '("==" "===" "!=" "->" "-->" "=>" "=="))
;; Enable individual ligatures only for specific programming modes:
(ligature-set-ligatures '(python-mode rust-mode c-mode)
'("||" "&&" "::" "->" "=>" "!="))
;; Enable ligatures only for HTML / XML:
(ligature-set-ligatures '(html-mode nxml-mode web-mode)
'("<!--" "-->" "</" "/>"))
;; Enable global ligature mode
(global-ligature-mode t))
