Understanding how to add storage for custom SoM made with Xilinx FPGA SoC with ARM A9 as Hard Core
When you are designing your first board with the selected SoC you should always check out the evaluation boards with that SoC. In this case, you can check how it is implemented in the Zynq7000 SOMs and boards with available schematics, like the Zedboard, Minized, Microzed. If you want big storage spaces, filesystem and data transfer to your PC, the best place to go is petalinux.

Question: You can have a QSPI Flash (32 or 16MB) for the u-boot, fsbl and the bitstream and a 16 or 32GB eMMC or SD card for the data on which you can configure a FAT or ext3 or ext4 filesystem with Linux easily(fdisk utility)
Question: in Linux you can configure CMA regions to read from and write to a file in the filesystem (this is done with DMA transfers as well but this is done by the kernel)
Question: For data transfer you can use a Ethernet interface, connect to you PC and setup a NFS between the Linux running on the SOM and your PC