When you run SH3 Commander you are saying it does not look like the image linked below? Just trying to be clear....
http://www.subsim.com/radioroom/down...32_e6q_irS.jpg
I installed SH3 Commander in its own folder on my C drive then ran the exec file to update SH3 commander to run with GWX 3.0. Next under options ( the wrench Icon I pointed Commander to the where I have SH3 installed. Started a new career ( won't work with existing careers you may have already in SH3 ...must be a new career), set my flotilla, start date, boat number etc. Then went back to options and set the gameplay features I wanted. Clicked the check mark icon and Commander started SH3. Once Commander had loaded SH3 I selected the captains name I selected in commander then selected the new career option in SH3 and made sure the starting year and Flotilla where the same as I previously selected in SH3 Commander...from there to the office and patrol....you won't have access to the crew options under "click for available options" until that point. You would have to exist and save in SH3 before being able to mess with the crew in SH3Commander If you have done the same but are still having a problem I am guessing that it is an installation problem