I thought writing in the flash was an easy thing
No.
maybe it would be better to write processes in the EEPROM
That is easy, but you can't execute code from EEPROM.
Anyone of you have idea if this would be easier to implement in a PIC (18F4550)?
I'm not that familiar with PICs but the basic principles are the same so I can't see it being any easier, but maybe.
It is being used for the rest of my classmates and it seems they are not having so much problems... =/
Maybe they are asking different questions. I can't believe they are writing a multi-tasking OS for this, yet that seems to be what you want to do.
as blinking (two) leds at different frequencies is enough for the purposes of the course I think size wont be a problem (Am I right?).
You can load parameters into EEPROM and perform different actions based on them, but you can't load code. You could even load a script into EEPROM or RAM and interpret that. But with these small AVRs you cannot load executable code anywhere unless you write a bootloader.
Maybe you should explain exactly what you need to achieve rather than assuming that writing directly to the PC is the way to go.
Rob