Personally, I never overwrite game saves. My first save on a new career is always Patrol 1. The next is Patrol 1a, then Patrol 1b and so forth and so forth, until I'm back in port. Then it's on to Patrol 2. Nothing complicated, no dates to discern or anything else. Just something to differentiate between each save. I have yet to reach the end of the alphabet.
I use CCleaner on a regular basis. I like to use it to wipe the free space clean too. I also use the Jv16 PowerTools by Macecraft regularly. I have never had a problem occur after using either of those tools.

Yet.