Does anyone know how to take actual C code and program directly to Arduino through the USB Serial Port? Do I need one of those programmers? I have downloaded AVR Studio 4 and WinAVR but need help on how to use them.
Also, will programming in C mess up the Arduino bootloader?
Out of the box, you program Arduino in C++.
If you want to develop for Arduino in C, you have to use a different IDE and a hardware programmer.
Most likely you'll overwrite the bootloader, so you won't be able to program via the Arduino IDE anymore (unless you re-burn the bootloader to the chip, of course).
Out of the box, you program Arduino in C++.
If you want to develop for Arduino in C, you have to...
Since C++ is a superset of C, you don't have to do anything but fire up the IDE and start typing.
The IDE adds some code to your code, like function prototypes and a main() function. So, you can't have your own main. There are certain C objects that don't make sense on the Arduino, like FILE handles.
@iRagDoll
What is the problem with the Arduino IDE that you are trying to use AVR Studio 4 and/or WinAVR to solve?