amiga disk files are 880ks. you need to compress them before writing to floppy.
cover the empty hole on a 1.44 floppy with a sticker (not the write protection hole). format the disk with the command
format /T:80 /N:9 a:
on your windows. get lha from aminet. get adf2disk from aminet. extract these on your pc and put them into your floppy. get a adf and compress it with lha. put it into floppy. now boot workbench and put your floppy into your a600. put the lha somewhere on your path (usually, workbench:c). extract the adf file to ram: (well, anywhere else is also ok.). put a formatted floppy into drive. write the adf to disk with the adf2disk command.
when you get tired with all compressing and stuff, get yourself one of
these. you can read compact flash cards on your amiga with the help of cfd and fat95 utilities found on aminet. a600 is a great kit for writing adfs.