Make a folder like "Standard Crew" with subfolders data\Crew-folders
Copy your files as you want to the folders and copy the entire "Standard Crew" folder to your Silent Hunter III - MODS folder. Now it's JSGME compatible...
To make it easier to use than explaining, you can find one here with standard files and no medals. Use that as a template and replace with images you prefer.
http://www.megaupload.com/?d=YERX63LE
Makes a major difference re. framerate as you've discovered.
AFAIK it's not necessary to be in port to make the change as it's only graphics files, but to be sure you'll have no problems, do make a backup first - or wait till in port.
The changes won't affect your crew's ability as it's only graphics changes.