The phases will more than likely be timed relative to each other and to the master clock you provide, but whether or not that reduces noise will depend on your particular design and layout.
The idea of a multi-phase controller is to improve efficiency by reducing the I2R losses in each channel, and to reduce ripple voltages on the input and output by increasing the effective switching frequency. The phase relationship between channels might result in destructive interference at some harmonics of the switching frequency (ie. good for EMI), or it might be constructive. Often there's a pin you can strap to set the phase relationship between channels, which you may want to be able to control when you go EMC testing.