Well after a bit of messing around I came up with a method to do what I wanted, this may help others out.
I wanted to add the "/sos" switch to my Windows 2000 entry so this is how I did it.
You need "CHANGEINI.EXE" which you can get from
http://www.thorprojects.com/files/chgini02.zipBOOTINI.BATCODE
@PUSHD "%~dp0" & ECHO OFF
@SET BOOTINI=%SystemDrive%\boot.ini
ATTRIB -A -H -R -S "%BOOTINI%"
COPY /Y "%BOOTINI%" "%BOOTINI%.old"
FOR /F "tokens=1 delims==" %%i IN ('FINDSTR /I /R "Microsoft Windows 2000 Professional" "%BOOTINI%"') DO (
CHANGEINI.EXE "%BOOTINI%" "operating systems" "%%i" "\"Microsoft Windows 2000 Professional\" /fastdetect /sos"
)