Im a Indep contrator. Have to file amended 08return and entire 09return. How do i pay in as little as poss?

irs kept 4200.00 of 2010 return. Irs said it was for 14k that wasnt reported in 08. but also they want me to file 09. made under 20k both yrs with tons of deductions. How do i give them as little as possible. And maybe retrieve some of this yrs return? thx a millon!