Go to controls, user interface, and scroll down to the bottom. Set "Activate Weapon Group 1" to 4 to your number keys 1-4 respectively. 4 is enough for fighters and bombers, some capital ship load outs might require more.
Now, in game press 2 and set your SNAC to this weapon group, set your MR to weapon group 3 and CM to group 4. That works for me with all my bombers.
Always remember to select weapon group 1 before you dock, and if you die with any other weapon group selected other than weapon group 1 you'll have to reset that group.
The advantages of this is if your opponent blows off a piece of equipment, it doesn't move your SNAC down from 7 to 6 or whatever. Also, it helps you aim your SNAC better because the crosshair will adjust to compensate for the slower projectile speed of the SNAC.