I believe - while this has been requested (module storage) it hasn't been implemented. So you need to mod every module on every ship.
Would be a darn good idea and its worth keeping sticking it on the suggestions thread.
if i am wrong i would gladly be corrected!!!
Module storage was implemented a while ago now. a maximum of 60 modules, at the moment, can be stored. And then transferred, for a fee, to whatever station you happen to be at (if it has outfitting hangar of course).
If the other ship can fit the module there is nothing stopping you swapping it between ships. I did this for a while til I had some extra modules pre-modded.
You can just buy em and store em in your 'home' system, then transfer the stored modules to the engineer base when you get there (does come with a credit fee tho) so you don't have travel back and forth. when delivered there you can mod away and swap em round at will.