You have a 5500 iirc (sorry, long day).
In that case you need two files: initrd.bin and zImage (case shouldn't matter, he says ;-).
I always tend to make sure that these are the only two files in the root directory - extra directories seem to be fine, but it may make a difference if they have certain names. Off the top of my head I think that bootflag (with some or other extension) will be flashed if it exists, so don't name anything with this name.
The short answer is that to be safe, directories are fine but no other files in the root directory.
Si
