When I did it, I used the SDK instructions and I was using Linux. I don't know about how you can do it on Windows, but since you were able to run dsedb, it seems like it may be possible. It may be possible to do with Codewarrior, but I don't know how.
In the same folder as the dsedb program there should be a tool called "dsflash". When I flashed mine, I used this command:
dsflash -d 10.0.0.10 /usr/local/sce/t10000-rel300.bin
You should replace the 10.0.0.10 with the IP address of your TOOL. When I used dsedb, I ran it like "dsedb -d 10.0.0.10". When you run dsflash, you should have the switch TOOL/WS switch in the "TOOL" position.
This takes a few minutes. After its done, you have to reboot the entire TOOL.
If this does not work for you, maybe try reading through the CodeWarrior documentation to see if can do this.