PIO core on SOPC builder?

What do you mean by custom driver? When you add a PIO core to the SOPC system, you can then just write to the registers to access the ports.

Include the altera_avalon_pio_regs.h file and use the IOWR_ALTERA_AVALON_PIO_* and IORD_ALTERA_AVALON_PIO_* macros.

EDIT: I think I understood what you meant after having sent the reply... If you want to have a specific device with read, write and ioctl calls, you should be able to do that by copying the folder C:\altera\8*\ip\sopc_builder_ip\altera_avalon_pio in your project ip folder and change the driver from there. You may have to change the class name in the ptf and tcl files to avoid a conflict with the actual PIO core.