Using atmega in arduino for other things.

Hi all, I just want to use the IC in my arduino for other non arduino related projects. I know it would be easier to buy another IC, but I can't easily buy one.
So I'm wondering how to use it with MikroC for example.
Can I upload an already compiled sketch from another compiler to arduino using USB?
Thanks

Compilers create executable code for specific hardware. If you are going to use another compiler, it must know about the Arduino chip, and be able to generate the correct machine instructions for the specific hardware.