Should I disconnect battery when uploading sketch?

I have an Arduino Pro Mini, and I'm gonna be hooking a 9v up to the RAW and GND pins. I want to know if I need to unplug the battery when I plug in my Sparkfun 5v Basic Breakout board to upload a new sketch.

I suspect it won't be an issue, but I know the breakout board also provides power, and I didn't want to risk overloading something.

You'll be fine with it plugged in. There won't be any overload. The 2 power sources meat in parallel meaning the voltage will stay the same but available current will be increased. Not that it would use that extra current.