Here's something very simple to get you started. It is possible not all surface pro 3's will be set up the same (but my assumption is they are), so maybe someone can let me know if it works for them? Make sure the three files remain together in a folder. Open 'enable' to enable the touchpad and 'disable' to disable it. If it doesn't work, try right clicking on devcon.exe and click the compatibility tab and check 'run as administrator'.
Its not the prettiest solution but it may be easier for you then going into settings.
edit: I downloaded my own file and it looks like windows doesn't like it. Gave me a warning, so I understand if you dont want to try it (you can force it by clicking on 'more info'). After you run it once, the annoying popup wont occur again. All it is is microsoft's devcon program and simple batch files which can be opened in notepad.