You might have noticed when you create entries in bcd using bcdedit, it assigns guid's to the entry, that you need to reference for any following settings you add.
By using a batchfile and som clever for, do command you don't have to type in the guid...
for /f "tokens=1-3" %%a in ('Bcdedit /store %BCD-File% /create /d "WinPE x86" /application osloader') do set guid1=%%c
Bcdedit /store %BCD-File% /set %guid1% systemroot \Windows
Please note that the second line has been wrapped and should be entered as one command...