Separately?
I thought you rolled 1 die for each aircraft, in this case 6 dice. If 2 hits are delivered, the defender gets to choose what gets shot down.
Text from Revised rule book page 25…
“Antiaircraft guns can shoot down attacking air units. Whenever an air unit enters a territory containing an enemy antiaircraft gun, the antiaircraft gun fires during the opening fire step of th combat. Roll one die for each attacking air unit (but ony one antiaircraft gun in a territory can fire, even if they are controlled by different powers). For every roll of a 1, one attacking air unit is destroyed.”
This tells me there is no distinction between fighters and bombers since they are all attacking air units. Roll six dice, defender chooses casualties.