You can use the front panel USB ports just fine. A motherboard USB header with 9 pins is actually two rows of 4 pins, plus one pin and an empty slot to provide proper orientation for a dual (double row) USB header. What you've got is a single USB port that is 4-pin and you can install it on the motherboard header as long as you're careful to get the ground correct.
In the image above, you can connect your 4-pin front USB connector to either 1-3-5-7 or 2-4-6-8 and it will work. Make sure the ground (usually the black wire) is on pin #7 or #8. If you have two 4-pin front USB connectors, you can connect them both to a single motherboard USB header.