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After I print my object in Repetier, the g-code 3D view shows red traces for part of my object. The only thing I've found in the documentation is that it means "Hot Filament". That seems to signify that the printer provided feedback to Repetier that the hot end was getting too hot in those spots. Looking at my printed object, I see that yes!, those spots got a little too hot and it melted a little. What should I do with that information? Currently I'm not using a fan as it prints so that would be one thing to do. Is there any smarts in the software that would take that information and lower the head temperature in those spots in the g-code the next time it was printed?

One thing you can do is to run the PID auto-tune again. It may not have a significant impact but if there was a modification made to the hot end, even an air flow change, it may need to be retuned. Hopefully, someone else will have a better idea.

I ran it again and it came up with much different numbers so that was a good call. When I went to put them in the EEProm settings, I found that previously I'd entered the extruder PID values for the bed PID values. Hopefully it'll work a little better now.