Are you trying to compile the source code? In that case you put it in the same directory as export template, the instructions are on my GitHub.
No, you use the application on PC. The .pck is file used alongside the binary (.exe on Windows, .AppImage on Linux or .app on macOS)
You seen to be thinking about automatic setup, next major release will be compatible with Nintendo Switch Online accounts, but I can’t really tell how long before support for Wii U (and 3DS) is implemented, as there have been no info or documentation about a public Pretendo Network API so far.