--- Quote Start ---
@Cris72
what you mean exactly with "configured your PIO for individual bit setting"?
2 bit-->2 output pin?
--- Quote End ---
You find this option in sopc builder: open the PIO module properties and just check the box labeled this way and rebuild system and fpga.
This feature is very useful in your case where you have to set/reset in different isr. Since you don't need the double step of reading the pio register and writing again with the changed bits, you won't bother if a higher priority isr changes same bits in the meantime (which could make a mess or pio status).
Regarding the other question about set bits separately, the answer is Yes: you read the register and simply change only the required bits:
led = IORD_ALTERA_AVALON_PIO_DATA(LED_PIO_BASE);
/* you can use any of these */
led |= 1; // turn LED 1 on
led &= ~2; // turn LED 2 off
led ^= 0x10; // toggle an extra LED possibily connected to 6th PIO output
IOWR_ALTERA_AVALON_PIO_DATA(LED_PIO_BASE, led);