You've got a drydock on your mothership, so you can dock the fighter in there, and build a single shield generator.
Then dock the shield generator into the drydock in the right place next to your fighter.
When the fighter undocks, the shield will stick to the hull in the fighter.
Spacedocks can do the same thing; its far more convenient than explosive bolts scaffolding and clamps, and that's what you pay the premium price to get a dock
Edit:
If you mean to weld an extra shield on to your mothership, then you can still do it, just pretend the drydock is a giant clamp.
1) Load a copy of your ship into the designer
2) Add the shield generator in the place you want it (make sure its connected)
3) Delete everything from the ship except the shield and drydock
4) Place a hull 1 segment in the drydock to grab, then delete the dock. (If you're building a hex shield, upgrade to a hull 2 segment and explosive bolt 2s.)
4b) For $20 more, you can add a capacitor 0 to the hull segment too, and the shield generator will have enough juice to stay enabled for the single turn before you weld it on and it starts to use the main ship's power.
5) Place explosive bolts to make the whole structure and shield generator connected
6) Save, build and dock the upgrade "ship"
The explosive bolts will collide with your hull and the edge of the drydock, and get knocked loose, but they're disposable and that's OK.
Or, since the drydock is so huge, you can just wing it, make a bolt string about the right length and then fudge the exact placement during docking.