I have been messing around a bit more with editing disk images and my IsoCobbler application. Here is a newer version (and source in Visual Studio 2010) now with some extra features.
There are commands like NEW, which allows you to start from scratch with a blank FAT formatted floppy image (the 1.44 or 2.88Mb variety). You can also LOAD and then EXPAND your existing 1.44Mb images and IsoCobbler will attempt to make them into 2.88Mb ones, trying to keep the boot sector working in the process.
After writing the EXPAND command, which needs to transplant the boot sector and hack it around a little bit, I decided to implement an MBR command as well. This allows you to put in your own boot sector, or save the existing boot sector from a floppy disk image. Anyway, for details of all the commands, see the "Help" file included in the downloads. This version still expects all the files to be in the root, it doesn't support folders yet (which might be next on my list actually).
So after all that messing about, I have gotten as far as building my own boot sector in x86 assembler (using NASM, The Netwide Assembler) which in turn boots into my own simple kernel (and when I say kernel, I mean Hello World application). IsoCobbler did of course make a bootable ISO out of that experiment, so I have a bootable CD that runs my own bootloader and then starts my Hello World code as the kernel. Umm, now I'm feeling the need to go off and write a 'proper' kernel (in C probably). It seems that making a program to help me build CD-ROM images has gotten all out of control, since I seem to be considering the idea of building my own OS as a consequence. Right, I'm off to visit Bran's Kernel Development Tutorial, I may be quite some time...