You custom field data is saved into the database just like any postmeta value… mostly. Fields on options pages, repeaters and some other places are stored differently or in other places.
If you’re going to bypass WP for showing the front end then I’d suggest digging through the database to see how all of your fields are stored and where. Doing a search using phpMyAdmin on you field name will get you to the areas you need to look at.
Is there a particular reason why you completely bypass WP on the front end?