You make sure all ligatures have widths that are integral multiples of the standard width.

If you’re strict, you make them the same width as the separate characters would be. If you’re less strict, you could, for example, have “⇒” or “½” be one character width, and not 2, respectively 3 (the latter probably would make you give up making a ligature for “1/2”)

Monoid also experimented with using ligatures for better kerning at some point, don't know if it still does that. I thought that was a neat idea, especially since that is kind-of-but-not-really what ligatures are for in the first place.

https://larsenwork.com/monoid/

The same way as in any other font. https://github.com/tonsky/FiraCode