Thanks, append the batchjob in the "Build Solution" was a good idear.
I Update the batch-file on GitHub
Now you can add a "post build command" in the "Build Event" (Debug and Release)
"$(DevEnvDir)\BossacArduinoDue.bat" "C:\Program Files (x86)\arduino-1.5.2\hardware\tools\bossac.exe" "$(OutputDirectory)$(OutputFileName).bin"