Best way to configure root file system in an embedded linux environment

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I am developing scripts for my embedded board ( a zynq board) and I need some scripts to be loaded prior to login. Since the filesystem is loaded into DDR memory, any modifications will be erased after a reboot. So for my development, I have to remove the SD card, then mount the filesystem on my development machine and after that, I have to unmount the FS and wrap u-boot headers on top of it. Finally write everything to SD card and see if everything is working or not. I was wondering if there is any better solution??? like reloading file system while linux is running???

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