updating/patching methods

Developing a touchscreen application for a vehicle... I'm trying to figure out the best way to put out updates for my application. A little background, I've only used ClickOnce one time before.

Using ClickOnce in this situation doesn't seem efficient, nor does copying/replacing the entire contents of the app multiple times a day. I've never done anything that involved byte placement/replacement (patching iirc). Is it sufficient enough to make a separate program that monitors usb ports, and when the 'newest' application folder is found, it will ask to update, close the program, patch, and reopen the program?

I've been reading as much as I can on patching, but a lot of links lead to autopatcher programs to buy and not a lot talk about learning the concepts. The only good link I have read shows an example with replacing 1 byte at some offset. How do you find which offsets you need?

Maybe there's an easier way to update?

If I do make a separate program that copies/replaces the entire contents for the time being, and add the new updating program to my main program, are they still considered separate programs? They are allowed to run independently, but will be installed in the same directory together (making it easy to locate the main program)?