The Space Shuttle had the ability to launch Centaur booster stages stored inside of the Shuttle during launch. How was this stage fueled, being fueled with cryogenic fuels?
It was filled through the "T-0 umbilicals" (referring to the time of disconnect).
LO2 through an umbilical on the Orbiter boattail, LH2 through one in the midbody.
This schematic shows the plumbing from the umbilicals to the Centaur through the CISS (Centaur Integrated Support System).
Challenger and Atlantis were modified to accommodate Shuttle-Centaur (providing ports from the exterior of the orbiter leading to the interior payload bay); the Centaur Integrated Support System (CISS) in the payload bay provided the plumbing from the orbiter to the Centaur itself.
The CISS provided all of the mechanical, electrical, and fluid interfaces between the Centaur and the shuttle. The CISS not only supported the Centaur during space shuttle flights, it also provided the means to control and deploy the Centaur. With the cargo bay doors open, the CISS would rotate (pivot) the Centaur up and out of the cargo bay and then release it. The CISS was designed to be reusable and returned to Earth inside the shuttle cargo bay. Both versions of Centaur with the payload/spacecraft and the CISS filled the entire cargo bay of the space shuttle. The two space shuttle orbiters designated to carry Centaur, Challenger and Atlantis, also had to be modified for Centaur.
From the Shuttle Centaur Project Perspective:
so, 4 connector panels on the sides of the orbiter, for various fill and vent connections. Apparently, Challenger and Atlantis were to be modified to carry the Centaur.
That image seems to be an annotated version of this (which doesn't show the connector panels):
The panels aren't evident in museum photos of Atlantis. They might be behind covers though.