When you end a patrol and get back to the office click on the crew managment, the crew photo on the desk or the sub and go to the crew managment screen, grab wounded or dead crewmen with the mouse and drag them to the left side of the screen, a window will popup asking if you want to dismiss that crew member, say yes.
Now grab a fresh crewman to replace the one you removed and drag him to the slot on the sub...be sure to pay attention to the crewmans skills and renown costs.
Hope this helps
