How to setup SAM3x8e IRQ handler for USART?
There is generally only one interrupt handler per component, so yes, you will have to check the status register to see what happened.  As far as setting up an interrupt handler, the chip has a register that needs to be pointed at the interrupt table somewhere.  I'm not sure how that would be set up with your libraries; it could be taken care of in the linker or there could be a library to manage the table.