Hi. Thank you for kind words.
That message from JGSME is nonsense actually because, both mods' files will go different location, and those mods won't interfere each other but Liveries folder is the main level for almost all cockpit mods. JGSME may not able to handle with it but, as a result you should say "yes."
On the other hand, I advice you to use OvGME, not JGSME. At least OvGME won't make problem like this.
See you mate.