How to understand Android 5.0 internal memory usage? I have a Samsung Galaxy S5(SM-G900F) which should have 16GB eMMC as an internal storage:



Are Android OS system files stored on the "System memory" portion of this internal storage? Or is there a separate non-volatile, but writable(because phone supports OS upgrades) memory for this? Is this internal memory partitioned? What is the difference between "Used space" and "Miscellaneous files"?
Samsung simplifies the breakdown a lot more than stock Android (I'm using a Moto X 2014) but I can help you understand what each portion of your storage is used for.

Total Space: Obvious, but going to cover it any ways - this is the total amount of storage space your device provides for ALL it's storage needs. This will be broken down into the sub categories below.

System Memory: The definition of "Minimum amount of storage space required to run the system" is an over-simplification, but it's correct. This memory chunk contains the portion partitioned to hold things like the kernel, bootloader, recovery, and (Samsung-modified) Android system files. Also contains whatever modifications the manufacturer shipped with Android (in your case, all of Samsung's proprietary apps and features). This isn't some special type of memory for these files, just a separately partitioned part of your available 16GB. 

Used Space: This is the part of memory dedicated to self/Google installed applications (not the pre-installed Samsung ones). 

Cached Data: This is the part of memory dedicated to storing the cached data apps use to function. 

Miscellaneous Files: This is essentially data stored on the device that isn't an app, an app's cached files, or Android system files. Things like music, videos, pictures, and anything else you throw onto the storage via USB or some sort of FTP ends up here. Some apps also create folders to store large amounts of non-cached data on the device, that will end up in here too. Feel free to tap on the "Miscellaneous Files" to see a basic breakdown of folder and data that fill this portion of memory.