[Q] Difference between flash-all.bat and system.img flashing when upgrading Lollipop topic

Hi All,

Since rooted, I am trying to upgrade my stock and encrypted Nexus 6 from 5.0.0 to 5.0.1 manually by flashing the factory images. My aim is to do not wipe personal data such as apps and photos. Since I am new to flashing, can someone please explain the difference between the "flash-all.bat" and the "system.img" method?

I have done a similar upgrade on my stock, rooted and unencrypted Nexus 5 by modifying the flash-all.bat file from "fastboot -w update" to "fastboot update" to do not wipe personal data.