Windows Server 2012 essential partition size for C Drive we recommend is 60GB, if there's not much space on your boot partition, it's needed to download partition tool.
Partition Extender is the right partition tool for you to download for Server system, it focuses on extending partition no matter what disk map you have or what file system you have, NTFS or FAT, both of them are supported in Partition Extender.
Windows 2012 may reports low disk space if it has less space to well perform System, after carefully check the whole C Drive, you found there's nothing to delete so as to fix this problem. Many people make C Drive essential space limit to 32G, that's not a thing for first use or rare use, but when you use it frequently or stay login for a long time, system itself will make new files to consume left free space.
So that's why we made a suggestion of 60Gb on C Drive when you first installed. With the help of Partition Extender, Windows 2012 partition disk tool, we can extend C Drive with free space from other partitions.
Installation partition is the partition we install system in, might be C Drive, or other partitions, for multiple system fans, they can have many systems in one disk and in different partitions,
Partition Extender can extend Windows Server 2012 R2 installations partition, no matter the partition locates, in MBR or GPT disk, Primary or logical partition. The theory in Partition Extender is to reduce partition size or shrink partition in other partition, and extend low disk space partition with this space.
By the way, USBs are not supported in Partition Extender. To be more specifically speaking, device with no partition table in are not supported by Partition Extender. See limitations to Partition Extender