First I would like to advise you to double check the run key locations in the registry for any operating system older than vista, as it has been a long time since I worked on them, so there may be differences that I don't remember.
If I"m understanding your question correctly this batch script should do what you want. It gives you a simple menu to choose to add or remove a program from the run keys(startup), and then lets you put in the program name and path to the executable.
:begin
cls
@echo off
echo Program startup Utility
echo.
echo 1. Add Program to Startup
echo 2. Remove Program From Startup
echo x. Exit
set /p choice= Choose A Service:
if not '%choice%'== set %choice%=choice:~0,1%
if '%choice%'=='1' goto :addstartup
if '%choice%'=='2' goto :delstartup
if '%choice%'=='x' goto :exit
:addstartup
cls
echo/
echo/
echo Add Program to Startup
echo or type back to go to main menu
echo/
set /p keyname= Please State Program Name:
if '%keyname%'=='back' goto :begin
set /p expath= Please Enter Path to Executible:
if '%expath%'=='back' goto :begin
reg add HKLM\Software\Microsoft\Windows\CurrentVersion\Run\ /v %keyname% /t REG_SZ /d "%expath%"
timeout /t 3 >nul
goto begin
:delstartup
cls
echo/
echo Remove Program From Startup
reg query HKLM\Software\Microsoft\Windows\CurrentVersion\Run\ /s
echo/
set /p keyname= Please Enter Program Name:
reg delete HKLM\Software\Microsoft\Windows\CurrentVersion\Run\ /v "%keyname%" /f
timeout /t 3 >nul
goto begin
Alternatively if you just need to be able to add or remove the same program and don't need to enter in multiple program names or exe paths, then you can modify the script like this, and replace %keyname% with your program name, and %expath% with the path to your executable(without the %'s) and then save it. Make sure your keyname is the same on both add and remove.
You can also exchange the "goto begin" lines with "exit" if you just want to quit the script after the selected action.
:begin
cls
@echo off
echo Program startup Utility
echo.
echo 1. Add Program to Startup
echo 2. Remove Program From Startup
echo x. Exit
set /p choice= Choose A Service:
if not '%choice%'== set %choice%=choice:~0,1%
if '%choice%'=='1' goto :addstartup
if '%choice%'=='2' goto :delstartup
if '%choice%'=='x' goto :exit
:addstartup
cls
reg add HKLM\Software\Microsoft\Windows\CurrentVersion\Run\ /v %keyname% /t REG_SZ /d "%expath%"
timeout /t 2 >nul
goto begin
:delstartup
cls
reg delete HKLM\Software\Microsoft\Windows\CurrentVersion\Run\ /v "%keyname%" /f
timeout /t 2 >nul
goto begin