Hi Mick,
Programming is via the marked UART0 pins only, this is because the UART bootloader runs from ROM so there's no way to reconfigure these pins. However, once your program is running you can use the GPIO Matrix functionality to reroute the UARTs to any pins.
The other pin labels are for using "IOMUX" to choose pin functions, which is less flexible so less useful now that it's possible to use the GPIO Matrix instead (it is necessary to use IOMUX for very high speed / low latency signals, but there is no downside to using GPIO Matrix for UART signals.)
The technical reference manual Chapter 4 explains the GPIO Matrix & IOMUX in detail:
http://espressif.com/en/support/download/documents
Angus