mkisofs makes an image of an iso file system that can be written to a cd or dvd.
Now a cd or a dvd is treated as a drive and as such it has an unnamed root
directory which in turn can contain subdirectories a any depth.
So: create an any handy hard drive, say d, with enough space a directory called
(say) root. In that directory, place any files you want to go in the root of
the cd or dvd. Also in that directory, create any top level directories you
want to appear on the disk. Proceed to copy files to these directories and
create subdirectories and copy files until you have the complete contents of
your disk all *** off of the directory root.
Now, suppose you have put the boot floppy image in d:\root\bootstuff\image
Then your mkisofs2 command should look something like this:
mksiofs2 -V volid -b bootstuff\image ... -o x:\image.iso d:\root
d:\root is the source path, the dots represent any other options you need and
x:\image.iso will contain the iso image that you burn using cdrecord2.