Running atmega 328p on 3.3 v

well,
I placed the chip on the breadboard , and am giving power via the 3.3V on the arduino.
Would the external clock being 16MHZ have anything to do with this problem?
also, when we use this method, does the booloader really get burnt into the chip, or it just sets the fuse bits?
I am asking this because I cannot program the chip using arduino directly anymore, I have the use my usbasp programmer.
However if i reflash the bootloader for the arduino uno, then i can program the chip using arduino again.

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