1 - Fly to system where you want to mod ships using your longest jump range ship.
2 - Dock at nearest station to the engineer base
3 - Request transfer your other ships to that station (*)
4 - Mod your current ship.
5 - Go back to the station in (2) and swap ships.
6 - Repeat between (4) and (5) until you have upgraded all your ships.
(*) "ah but ship transfers cost a lot of cash!!" -> no longer a problem, as missions are now paying gazillions of credits all over the bubble.
Oh and hurry before FD puts the engineer commodities back.