Editing binary before writing to AVR controller

I want my binary to contain multiple instances of the C code I wrote, so I can check them against each other etc. I'm using an STK500 to program an ATMega16 at the moment. What would be the easiest way to do this?

Thoughts: As of now I think, the easiest way would be to just take the ELF-file, blow it up to the program memory/flash size of the controller and manually do padding with NOPs, so my 2nd/3rd code-instance starts at the desired address. Since I know nothing about ELF and very little about uC-programming in general, I suspect I can't just open the ELF file and copy-paste + fill with NOPs... ??