I might be able to help you out- I fly all the time and have a pretty good system I use.

Which is your higher priority, a non-stop flight or lowest price?

[edit]
Also, out of the hundreds of flights and connections I've been on (all economy with the cheapest carrier I can find), I've only had one single issue with baggage. And that was when I got to the airport so late my bag didn't make it to the plane before takeoff. Entirely my fault. I got it the next day, though, so there was really no problem in the end.