ah, so youre using a dummy primary and just sticking the secondary points over the holes for the pod tubes? ah whatever works. i use the existing vwep system for gatling guns and externally mounted missiles. its preferable to me that ships have fewer missiles, and rocket pods are a deviation from that.
anyway by deciding that a certain bank is external, and using divided selection lists, you can implement a system of combined external and internal hardpoints. the first point in the bank is always for a large bomb, with the cargo size equal to the bank size. this ensures that only 1 warhead can be loaded. however if i add additional points, i can create a group of missiles surrounding the central point for big bombs, and i can make the cargo size for those weapons 1/n, n being the cargo size of the big bomb. so lets say i have a fat man at cargo size 50, but i have a smaller missile with a size of 10. on the ship, the first firing point is located right in the middile, this is the only point the bomb will ever touch, but i can place an extra 4 points around it for the smaller missiles. so now the point can handle 2 weapon configs. cool stuff.
you know a cool feature would be weapons subsystems for individual weapon banks or even individual firing points. like you could use a rocket pod subsystem, and if you shoot it, you destry the pod and those points associated with it can no longer be used. if you have 2 pods on the same bank, you can make only the destroyed pod be effected, and if you want to be really advanced, could loose all ammo stored in that pod as well. as a result destroying a pod would also destroy half your ordinance. same with prims, you could shoot off an enemy's guns. or just make the vweps themselves have their own hitpoints.