Reference number - is it my income tax ref or my PAYE ref?

I am not sure which number to use as my Tax reference number. The Income Tax Ref no and PAYE Ref No is available. My other question is: I received two IRP5's. Do I add the amounts for the different codes?

You would use the reference number when asked and the PAYE number when asked.

No, you would submit one IRP5 at a time - Register for TaxTim and let us assist you, we offer a service to import you IRP5s as well and then assist with submitting directly to SARS.