JMHO, use the brakes "together" as much as possible, If coming to a stop your can, "feather" the rear only to slow you down, (just slight pressure), it's best not to "clamp" on the front brake only as that might just jerk the handle bars out of your hands and put you down hard on the pavement. We just went to the LBS today as my wifes bike had a squeaky front brake, I asked them to check the "toe in", he said it seemed ok but there was a residue of some sort on the rim, that I didn't get off with my pre-ride rim cleaning. Who knows what it was but the brakes didn't squeak after he finished.
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Take Care, Ride Safe, have FUN! :)
Jo: 2009 ICE Trice T
BJ: 2011 ICE Sprint Special Edition