To the best of my knowledge all the Altera tools depend on a JTAG connection so you'd have to write some code that uploads the FPGA image and then burns it into the EPCS.
I'm assuming you're talking about the FPGA code, not the user application, although you can field-upgrade either one from your code.
The one thing to keep in mind is that the FPGA field-upgrade is a one-shot deal since there's no way to recover from a bad FPGA image in the EPCS unless you have additional logic like a microcontroller or something like the MAX chip on the Altera dev board.
Andrew