Arc. You need those weapons (the pdc wpns) to each have a different weapon family number. currently they all are in family number 6, (along with reactive armour I to III), just create a new family # for each weapon and put them in there. Currently the wpn family goes to 118. So if you give them #'s 119+ it 'should' work. Then you can use them in designs.
If this doesn't work then you have to add them to design by 'abilities', ie, point defense is added to ships by the 'point-defense' ability, mine sweeping by 'mine sweeping' and solar sails by 'Extra Movement Generation'. So a different 'ability' needs to be added (maybe point-defense1, point-defense2, etc), then you can add these in the 'misc' abilities lines. This should work (now that I think about it, this should work better than my above suggestion, I tried having pdc as a secondary weapon once, there were no extra pdc added vs a normal ship, so try this.)
If this does not work then I am smoking something and do not know what I am talking about. Try Dev, he might know. Currently I'm just pi**ing into the wind
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"The Empress took your name away," said Chance.
Owen smiled coldly. "It wasn't hers to take. I'm a Deathstalker until I die. And we never forget a slight or an enemy." -Owen Deathstalker.