I've now run a test where I:
* build my multi-file x64 app
* protect it using Vitual Box or Protector
* take the single-file-exe and add a payload to the end (by simply appending it)
* inside the EXE, my app asks for the "executable file" which is the real EXE (not the original virtual one)
* my app ...

Regarding #2, I just did a test and it seems that if you ask for the EXE file inside your app that's been protected, you will actually be given a file handle to the container EXE (e.g. the boxed / protected virtual app, not the original EXE file):

Notice how the original EXE is about 2MB in size ...

I have a 64 bit app which plays back a movie using a HTML player.
The files structure looks like this:

https://xochi.com/xojo/pix/payload.png

Questions:

1. Is there any way that I can change out the payload AFTER I've boxed the app? In other words, I want to box the app, and then change the ...