I am in big s***, cos I have not paid yet my taxes for fiscal year 2008. I know it was last April 30th BUT:
No you aren't in trouble. Just make a transfer now and write a letter in which you explain why you didn't pay, apologise for not paying and express your active regret for not paying.
And if I have to pay, then what is the fine? guess some percentage over the total amount of what I have to reimbourse?
I would be very surprised if you had to pay any fine at all. The general rule with the Polish tax office is that if you go to them and confess your sins, they go easy on you; but if you try to screw them over and they catch you, they will nail you to the wall as a warning to others.