I use a total of 4 saves.
TDK1: 'in office' save after loading up the sub for the new mission
TDK2: start of new mission
TDK3: in mission
TDK4: in mission
Once my mission is under way, I overwrite TDK3 and TDK4 every five minutes until the mission is over. I did this with SH3 too. I've never had a corrupt save doing it this way.