Ok I'm running Wing Commander on Windows 8 through dosbox which I bought off gog.com. I am trying to figure out step by step how to install debug mode on all three. Also, transferring pilot records to all 3 as well. Thanks for the help.

Honestly I couldn't figure out how to properly work them all. I just renamed things in the files. The main file you'll be working with is dosboxWC_single.conf, and the line:

loadfix -1 WC1

just change it to loadfix -1 WC1 Origin (case sensitive) and debug mode is enabled, and -k after Origin (Origin -k) for invulnerability.

All I could do to figure out playing the secret missions was changing the lines to

loadfix -1 sm1 and loadfix -1 sm2 when I wanted to play them in order.

Bringing in pilots to them is basically just in the gamedat folder so just lead to that folder when the time comes.