I'm just getting rolling with engineers, and there's a lot of advantage to being on site with the engineers instead of just using the pinning blueprints and using them remotely.
So it seems to me that you could do this:
1) Wherever you've set up as 'home base', get in each of your ships, and store the modules you want to upgrade.
2) Fly to the engineer's system, using your ship with the highest level slots.
3) At the engineer's site, go to ship outfitting.
4) Transfer all the stored modules from your 'home base'.
5) One at a time, install the modules you wanted to upgrade, upgrade them, and store them again.
6) Fly back to home base, and then transfer all the modules back home.
If you have all the mats needed, you would only need to take the trip to visit the engineer one time, rather than flying a bunch of ships over to the engineer. The engineers don't seem to have shipyards (the ones I've visited have not), so you can't transfer your ships using the transfer function. The cost of transferring modules costs considerably less.
Helpful or no?