When you use a bonus bet to place a bet, the bonus bet amount (value) is deducted from the winnings. This is because the bet has not been placed with cash funds, but rather a 'free bet'.
To calculate your payout, use this formula: (Bonus Bet Amount x Odds) - Bonus Bet Amount
For example, if you use a $50 bonus bet on a $3 winning bet, your payout will be $100. The calculation goes like this: (50 x 3) - 50 = $100