Safely connecting a Microcontroller with a separate power supply to USB

Hi,

I'm working on a project with basically a home built breadboard Arduino using an Atmega328p. I've been powering the microcontroller from USB (using a FT232R USB serial breakout board) but am to the point now where I need more current than USB can offer. However, I still need to use the USB port to monitor results on a serial terminal coming from the microcontroller on my computer at the same time and occasionally reprogram.

So when I power the microcontroller with a separate 5v power...

Safely connecting a Microcontroller with a separate power supply to USB