using flashprogrammer to program application image

Are you planning to have two images in the flash?

When the FPGA powers up, it will always load the configuration at address 0 of the EPCS. If you want it to load another configuration, you need to use the remote update component.

For the software, the default bootloader included with the EPCS controller always load into RAM the software placed in the EPCS, just after the configuration at address 0. If you want to boot from somewhere else, you'll have to make your own bootloader, as explained in application note 458 (http://www.altera.com/literature/an/an458.pdf).