Worth noting that Garuda domestic no longer provides the additional sports baggage allowance of 20kg for free. They apparently stopped doing this in August which was a surprise to me in September. The process Elmer outlines is correct and very slow because both the checkin desk and then the payment desk will run calculations on total cost, and once paid you have to queue again for your boarding pass.
In a group of 8 divers we had 40kg each instead of the allowed 20kg. On the first domestic leg we were charged about $2.50 per kg extra. On the way home the cost was about a quarter of that for exactly the same bags. So either the weigh scales aren't working in Kupang, or smiling a lot brings down the charges (or both).
Don't frown or get angry - customer service people in Indo get upset and then everything gets harder. They always seem quite nervous about explaining that it's going to cost extra, so presumably some passengers must get stuck in. Lots of time and lots of smiles is the best bet.