You will (hopefully) notice four connectors on one end. Two will be for the 3.5" drive and two will be for the 5.25" drive. You will also notice that the cable has a twist in it between the connectors. The two connectors closest to the controller card and before the twist are the connectors for the "B" drive. The two connectors after that twist are the connectors for the "A" drive. That twist is how the drives know which one is wanted ("A" or "B").
What you now have to do, is take the 3.5" "A" connector and install it on the 3.5" drive and then install the 5.25" "B" connector on the 5.25" drive(remembering to observe correct polarity of course(pin 1 goes to pin 1 and all that)).
If, when you open your computer, your ribbon cable does not include the correct number of connectors, then you either have to forget about changing your floppy drives around or you have to go purchase a cable with the correct number of connectors. Most older systems will probably have only a 5.25" "A" connector rather than both a 5.25" and 3.5" connector.
This page is part of the Warp Pharmacy project - a project dedicated to providing comprehensive support for OS/2 Warp via the World Wide Web.