An AVR with the bootloader loaded ALWAYS runs the bootloader. Normally it will look at the serial port for a couple of seconds to see if there is boot traffic, and if not, start the sketch (blink.) So it's just a matter of timing a press of the RESET button correctly. (The amount of time that it waits is dependent on the actual version of the bootloader that you loaded. The old ATmega8 bootloader would wait something like 10 seconds. The optiboot distributed with Uno waits about 0.5 s!)