I'm working on my chicken flauta recipe skills today, I like to make everything from scratch but all I can find are recipes with store bought tortillas.   Knowing how much better homemade corn tortillas are I'm thinking of trying this with scratch made flour tortillas, stuffing and then frying.   My question is should I first cook the flour tortillas in a pan, then fill and fry?  Or fill and fry with the raw dough after pressing it? 
According to this page... neither your first option. You should toast them in a pan without oil.     After rest period, heat a large pan over medium-high heat. Roll each   dough piece into a rough circle, about 6-7 inches in diameter, keep   work surface and rolling pin lightly floured. Don’t stack uncooked   tortillas on top of each other or they will get soggy.      When pan is very hot, place one dough circle into pan and allow to   cook about 1 minute or until bottom surface has a few pale brown   spots. The uncooked surface will begin to show a few little bubbles.   If tortilla is browning too fast, reduced heat a bit. If it’s taking   longer than a minute to see a few pale golden brown spots on underside   of tortillas, increase heat a bit. Flip to other side and cook for   about 30 seconds. You want the tortilla to be soft but have a few   small pale golden brown spots on surface. Remove from pan with tongs   and stack in a covered container or zippered bag till all tortillas   are cooked. This will keep them soft and pliable.   You can view the complete recipe following the above link. 