Well, that would be the case I guess. I wanted to see if I could use PWM on timer 0 (pin 5 I believe) while still maintaining millis() and such. It sort of seems to work, but I need to change the prescaler for my project. So I would adapt the prescaler with TCCR0B, and set the prescaler variable with a function. There might be a small glitch in the millis() function, but that won't be a problem.
I'll try this weekend, thanks for your input !