The links should be automatically handled by Sigil. Or calibre's editor -- in fact, it has a very nice autocomplete fuzzy-matching thingy.
As far as the file extensions thing goes -- As DiapDealer said, it doesn't matter. The file needs to be valid xhtml (or else you know because Flightcrew or Epubcheck yells at you

) but it happily treats .html or .htm as .xhtml --although nitpicky perfectionists like myself

seem to have congregated in this thread here:
https://www.mobileread.com/forums/sho...d.php?t=257089
Totally optional, no one will ever know or care other than you... I wouldn't even bother if I were you.