Add your program in the registry:
Run - These are the most common startup locations for programs to install auto start from. By default these keys are not executed in Safe mode. If you prefix the value of these keys with an asterisk, *, is will run in Safe Mode.
Registry Keys:
HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Run registry key
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run registry key
Then you can launch your batch in an invisible mode:
wscript.exe "C:\yourpath\invis.vbs" "your_file.bat"
In invis.vbs put...
CreateObject("Wscript.Shell").Run """" & WScript.Arguments(0) & """", 0, False