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))