Missiles gives you flexibility, you can target smaller ships that are hard to hit with your other guns and if not hit them at least force them into evasive maneuvers which can give you the upper hand. They have good range and do not require much in terms of aiming.
3 cerbs are good if you are deadly accurate and good at dodging at 2-3 k range. You might find that some cruisers seem impossible to hit with them.
Mortars, I don't like them in general but I know some do. They are good in a support role in fleet combat when you can snipe an unsuspecting enemy cap, but in a 1-vs-1 your enemy can easily dodge the slow projectile.
I'd go with the setup you and Flash are using - I've been killed by that plenty of times
OK, I will stick with the setup I have then So, right now I have the secondaries in weapon group 1 with 2 secondaries in weapon group 2 for fast firing, i have the primaries and cerbs together in group 3 and it seems to be ok but I'd love to have some input on setting them up better and possibly some pointer on when to fire what. Also i noticed that the "E" key fires flaks and missiles. Is there a way to set it to only fire flaks, or only fire missiles?
no, but the missile fires on your cruise disruptor key (middle mouse button/scroll wheel in my case).
people have different setups, but the way I do it is like this (I use it on snubs too, so its universal):
Weapon group 1: Secondaries
Weapon group 2: 4 x Primaries
Weapon group 3: 2 x Primaries (for when I want to preserve energy)
Weapon group 4: Empty
Weapon group 5: Cerbs (and I have "Fire Weapon Group 5" mapped to my mouse's thumb button so I can fire cerbs while I have primaries selected)
Weapon group 6: Flaks (mapped to another mouse button so I can always fire it quickly)
So you can use the weapon groups and the "Fire Weapon Group" key setting in the options menu to map it to a button that suits you.
Weapons Group 1: Secondarys
Weapons Group 2: Flaks
Weapons Group 3: Missile
Weapons Group 4: Prims and Cerbs
Weapons Group 5: Prims
Weapons Group 6: Cerbs