I didn't actually program it, but I did watch an analog computer being programmed when my father took me into his work. Programming was done by connecting patch cords with banana plug ends to patch panels on 19" racks. Various op amps were connected with LCR networks and other analog functional blocks to simulate physical systems. Output was on a pen chart recorder. Around 1960.

The program I remember was able to simulate the response of an airplane (or car, different version) to simple control inputs--and since it was analog it worked in real time!

Have had a fascination with banana plugs and other patch cords ever since...