Four things:
First know the range brackets for your Photons. Photons always hit from range 0-1 but as you've noticed, you will take feedback damage to your shields. Out to 2 you have a 5 in 6 chance of hitting. Out to 4 you have a 2 in 3 chance of hitting, and out to 8 you have a 50/50 chance. Out to 12 you have a 1 in 3 chance of hitting, and then out to 30 to have a 1 in 6.
Second, you have alternate weapon modes for your Photons. Which are available on the MFD for the torpedos. The first Weapon mode is overload, which double the damage of the photon, but double the power requirements for them. The hit profile is exactly the same as the standard Photon, except if will not fire beyond range 8.99 (which for game terms is 8 ). The second is Proximity. These are the same type of warhead as the standard Photon (same power requirements) but does half the damage on impact. They cannot be fired inside of range 8, but do have a 2 in 3 chance of hitting out to range 12, a 50/50 chance out to range 30, and a 1 in 3 chance out to range 55.
Third, Photons are VERY vulnerable to ECM. If the F5 has a 1 point ECM shift, you basically now have 1 in 6 chance of missing at point blank, and a 1 in 3 chance of missing at range 2. The odds steadily decline in his favor. If he gets a 2 point ECM shift, you might as well not fire the photons. (you can still hit, but the odds become even worse for you) Try to counter his ECM with ECCM of your own, using the EW panel. The MFD panel right below your sheild panel.
Fourth, His missiles (drones) will always hit, but unlike your Photons, you can shoot down or even hold those missiles away from you. When he fires his Missiles, use the 'V' button to toggle your tractor beams to defend you. These tractors will grab the incoming missiles and hold them away from you, while your Phasers recycle to destroy them. If you have a Phaser bank standing by when the missiles get within range one, the Phasers will automatically shoot at them to attempt to destroy them. And unless they are Mark IV Missiles, one Phaser shot is usually enough. Your CA will have 2 defensive Tractors. Now, a problem that they fixed in SFC2, but is still present in SFC1, the V key only activates your tractors (in SFC2 the V key is a toggle). To get your power back you have to go to the defense panel and turn off your defensive tractors.
Hope that helps.
Edited... darn sunglasses smiley, who the heck thought that smiley was a good idea, I always seem to end my parenthetical notations with an 8...