On the Tool, in the home directory, which you should be in, if in doubt type ls to list the file present, do "md5sum t10000-rel300.bin"
On your windows machine, get some utility to calculate a md5 hash, find one on google...
The hashes should be identical for both files.
After that, you'll need to use dsflash as explained in the setup.pdf but without needing an IP address and pointing to /home/t10000-rel300.bin
Dsflash should be in /usr/local/sce/bin, go in that directory, type ls to list the files to check if it is.