Most installers will allow you to append to the system path environment variable. Check the documentation for this feature.
If you're installing manually, you can use setx.exe (from the resource kit IIRC) to modify the path - but be careful, you do not want to replace the existing path with just your app's directory, he said with experience :)
Or, my favourite, use WMI in a script:
eg.
strComputer = "."
Set objWMIService = GetObject("winmgmts:\\" & strComputer & "\root\cimv2")
Set objVariable = objWMIService.Get("Win32_Environment").SpawnInstance_
objVariable.Name = "Path"
objVariable.UserName = "System"
objVariable.VariableValue = "c:\myapp"
objVariable.Put_