You either set them on interception (fortify=same thing, less flashy?) and wait for them to strike (intercept has a radius around your city, bait them with units) or you just use your planes against a city that has them. Usually what I do against a city I'm about to attack is let my Fighters go first: they'll usually fight against the enemy fighters, then I send the Bombers, which have less chance to intercept, but sometimes they do if there are still fighters around. The AI doesn't usually go crazy with Fighters, like having 4 of them at a time, but 2 Jet Fighters can take down or cripple your entire Bomber force if you lose the Advanced Flight race.
BTW, promote your planes so they have better chances.