What I did was to copy the directory gog games then I renamed to copied directory to WCG
renamed the sub directory wing commander 1 and 2 to wc12

Launched dosbox and typed
mount c "\wcg"
C:
cd wc12
cd wc2
wc2

and transferred a character from secret missions 1 when it asks for the path I enter
c:\wc12\wc\gamedat and my pilot transferred.

since the c drive is mounted as wcg you do not need to enter that in the path

To sum:
Copy and rename gog games to wcg
rename subfolder wing commander 1 and 2 to wc12
launch dosbox
at the Z:| prompt type mount c "\wcg"
Navigate to the c:\ drive (just type C:)
navigate to your wc12 folder (just type cd wc12)
navigate to your wc2 folder (just type wc2)
type wc2
at transfer pilot screen
enter c:\wc12\wc\gamedat

Shortcuts made