Doh! As far as I know, Mame Analog+ will work with multiple mice under Windows 98se, but only if they are all USB. Mame Analog+ XP (on the other hand) uses a different system which has the ability to mix-and-match usb/serial/ps2 mice, however that's only for Windows XP.
Your 2 closest options are:
Use 2 USB mice with Windows 98se & Mame Analog+.
Switch to Windows XP & use your ps/2 and usb mice with Mame Analog+ XP.
Also, you could run XMame or AdvanceMame under Linux, which also supports multiple mice of different types.