What needs to be done is for the floppies to be copied. There is a set of these disks that the system boots from. They are they same size as a 3 1/2 inch floppy for a windows machine. I don't know for sure that they aren't some weird format. Can these be copied using a Win machine? Or, using DOS, Unix...
Nope. Only an Amiga or custom hardware can read/write to an Amiga diskette. They are standard 3.5inch double density disks, but the Amiga uses a different data density (880k, instead of the PC standard 720k). This is accomplished by the Amiga floppy drive rotating the disk at a different speed from a PC/Windows 3.5" floppy drive. Therefore, the Amiga and the PC 3.5" data formats are hardware incompatable. (Think 45rpm records vs 33rpm records, only in digital you don't end up with the "chipmunks" you end up with sheer garbage read/written to the disk.)
So, in other words, you can take a standard DSDD (non-HD) 3.5" floppy diskette and use it to backup your data to, but you'd have to MAKE that copy on real Amiga hardware, or the "Catweasel" hardware. (WinUAE and other emulators are also unable to read/write to real Amiga disks, without custom hardware.)
Cheer up, though. Making a copy of the disks on an Amiga is very easy. If your master disks are NOT copy protected, you can go to the Amiga system and open a CLI or shell (theres an icon for it) and type the command:
"diskcopy df0: df0:"
(without quotes) and then follow the instructions.
There are also a number of dedicated disk copying programs for Amiga. You'll need to find one of these, such as X-Copy, if your disks are copy protected.