But now I need a way to include it in my own windows software. I actually just want to copy some of the main function of the Flip-software (write, verify).
I do not (will not) use Atmel, but for the Philips chips the routines - as used in FlashMagic - are available from www.esacademy.com. I have no idea how similar the Atmel thing is but, if they do not want to release the code, the Philips stuff may give you some pointers.

Erik