If your BIOS only allows for one floppy disk drive then you have to choose if you want to use the 5.25" or the 3.5". This video explains the jumper settings. If you don't want to watch the video and want to get right to it, head over to http://ftp.epson.com/desktop/SD800.TXT for the full explanation of jumper settings.

3.5" 5.25"
Slot Connector SS1 (1.44Mb) (1.2Mb)
Configuration 1: Upper Drive A A A B
Configuration 2: Upper Drive A B B A
Configuration 3: Lower Drive B A B A
Configuration 4: Lower Drive B H A B