So I have transitioned several ATMega328Ps from the Arduino Uno R3 to a breadboard and they work fine. Once I move the chip, I replace it on the Arduino with another chip with a preloaded bootloader (product: http://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_2129334_-1). This is my microcontroller programming methodology, probably not the best, but it works fine. It's really cool to see a project working perfectly with everything on the breadboard standalone.
Now if I want to update the software, I could move the microcontroller back to an Arduino. But it gets difficult because it requires removing wires. Is there a way to reprogram it in place on the breadboard (and also on a PCB when I get that far) using the Arduino IDE? Thanks for any pointers.