I think those often come down to really understanding the language, and practice. Once you know what you are doing, it is much easier to know what to put down. The same applies to fixing bugs. Once you deal with it enough, you learn how to quickly locate them.

That said, organizing and commenting your code can be helpful. If a certain behavior is wrong, you should be able to directly jump to that area, rather than scanning through your code.

Keep debug on via #define debug whenever you're testing. Use the log to find runtime errors, and the profiler to watch out for anything too intensive. Although profiling is usually only useful when you have at least a few people actively playing.

I'd say back up your whole source once a day, or after any major changes. Delete old back ups daily as well, except on anything you think you might need to revert changes on later.

These are mostly just personal practices of mine, mind you, and I don't always do it all. I'm bad about not always doing the back ups. It's just something general that has helped me.