I think this will work better if the focus on the X-Wing games, with Armada just being the source of narrative. The thing is, I think that if the Armada game is being played conservatively by either side, then the X-Wing games will be too one-sided to be any fun. By conservative, I mean engaging the fighters with the outcome not in one's own favor.
I think to make it work, you'd have to alter the disengagement rules for Armada, and the outcome rules for X-Wing.
So, if snub- and superiority fighters are there to screen bombers, then the bombers should have some chance of escaping the X-Wing-level engagement by flying to the opposite side of the field.
That does seem more plausible with X-wing being the narrative. I was thinking some thing like if you are at range 1 and are engaged (Armada), then you play 2 rounds of Xwing. Any losses are recorded and "displayed" on Armada. Those squads are built from x-wing and kept secret from your opponent. After the xwing rounds all ships (xwing) are removed from the area (separate from Armada).
I understand this type of battle/game would take a long time but it would feel epic to me and if you didn't want to do a specific squad battle just roll or play as normal in Armada for that battle.