problem with HSMC

rx and tx are just conventions, you can use them in any direction you want. But you need to keep the pairs together if you use them as LVDS (i.e. HSMC_TX_p4 and HSMC_TX_n4 together, but not HSMC_TX_p4 with HSMC_RX_p11).

For the pins that you use as general I/O if you don't use LVDS you can use any pin as you want, as input or output.

If you have a lot of data to move from/to the PC, it may be easier to use the Ethernet port. The embedded USB Blaster only allow communication through JTAG, and you would need to use a virtual JTAG component or the JTAG uart.