How to boot from debugging on Arria 10 board(Custom board)

We customized an Arria 10 board, 

but booted it from emmc, the emmc
was soldered to the board and there
was no epcs.

For the first time, we can only use 

JTAG to program the FPGA’s sof files
and uboot.

There is only one JTAG, in that case,
can I use a JTAG to program two
different files?

Or can you use any tool to package
two files together? Can anyone help?