|It would be a good idea to get a boot loader, continually pulling drives in and out of a computer is going to reduce their life span. They were not designed for that kind of handling.|
Unlike Windows XP and later, Windows95/98 didn't come with a built in boat-loader so you will need a third party boot loader. The following link will give you some to chose from
The two Linux boot loaders, Grub and Lilo work well with Windows. However they come in source form and will need to be complied which may be beyond you means. However, if you can get hold of a copy of Linux they are usually included ready to run.
You can boot from a single drive with multiple partitions or two drives as necessary. All the boot loader is concerned with is bootable partitions and cares little if the are one single disk or multiple disks.
Bear in mind though if you boot to Windows 3.1 and the Windows 95 disk is formated to Fat32 you wont be able to read it as Windows 3.1 wont read a Fat32 partition. However Windows 95 is quite happy with a Fat16 partion that Windows 3.1 uses.