You can remove Kickstart ROMs with a small flat bladed screw driver if you are very careful, lifting a little on each end at a time until it falls out easily.
As for what format, it must be the Amiga OFS or FFS format, unless you plan to use a third party format such as SFS, or PFS. Do you have a complete set of Workbench disks? If yes, which version? The "Install" disk has a hard disk utility to format the drive and partition it. Most users choose a smaller 100mb to 500mb partition for the AmigaOS/Workbench as if there are any validation problems it will take much less time to correct than a 2GB partition. Then it is a good idea to keep the rest of the partitions at, or under 2GB unless you are using a more modern version of the AmigaOS such as 3.1, 3.5, or 3.9 with the 3.1 Kickstart ROM (version 40.68 or higher I think).
I don't think that your version of Kickstart ROM can recognize the FAT or NTFS file systems at all, but in any case, I am pretty sure you cannot use either of those file systems for your boot partition.
Edit: Looking at your situation again, with all the adfs you want to get on your hard drive, you might be better off formatting and installing the AmigaOS via WinUAE if all your adfs are currently on your PC hard drive. I have not done it, but others have. Since you have an A600 with a PCMCIA slot, it would be a good investment to get a PCMCIA to CompactFlash card adapter. That is how I move files from my PC to my A1200 or A600 and then convert the adf's back into Amiga Floppy Disks.
AmigaKit is a good source for the adapter and software to do the conversions.
