It depends on wich Gun you are going to use.
For example, if you have a weapon with a high bulletdrop (Heavy Flak,Lumberjack,Mortar) use Lesmokrounds in it to increas the range and making aiming easier for you.
Heavy Clips are good for weapons with a big bulletspread (Gatling,Carronade,Manticore,Small Flak and Banshee) all these weapons are mostly used in mid down to low range battles.
Burst Rounds are good on weapons with a big basic AoE (Manticore,Lumberjack,Mortar,Banshee) by using this rounds u can deal damage to a lot of ship components at the same time.
Incindary Rounds are uses to set ship components on fire, weapons wich are good for this ammo type should have a high rate of fire and big clip size (Manticore,gatling,Banshee).
Heatsink Rounds making your gun oviously fire proof and you get a bit more clip size for sacrificing a bit damage.
Greased Rounds sacrificing damage for a 60% higher rate of fire and 20% bigger clips, good on weapons with a good basic rate of fire ad big clips (Banshee,Gatling,Small Carronade,Mortar).
Charged Rounds sacrificing clip size and rate of fire for 30% more damage, wich is ood on all weapos with a good basic damage per shot (Heavy Flak,Lumberjack,Mercury Fieldgun).
The last one is the Lochnaga Shot it reduces your clip down to one shot removes recoil slows down the bullet and it deals 175 points of damage to gun wich fires it, but u get 150% mor dmamge out of this shot. At the momoent there are only three guns wich can really use it the Heavy Flak, Mercury Fieldgun and the Heavy Carronade.
All in all you should use the rounds to increas the benefits of the weapons and reduce the weaken of them while not sacrificing to much damage.
The rest is all about hitting the target, wich is a combination of motionprediction of your ship, the enemys ship and the bullet it self. Sounds hard but with a bit training you don't even have to think about it while shooting.
Another important point is the comunication with your captain, on some ships its hard for the captain to see if a enemy is in angle for your gun or not, (a working microphone is very useful on this point) so u can tell him/her "a bit more to the right/left/up/down".