See Flash block question on MK60FN1M0VLQ12? and more recently What is the flash block size in MK60FX512 (and similar K60)? 512K or 256K? for discussion of what the work "block" means.
Now for the actual question. Looking at the FlexNVM EEPROM application note AN4282, figure 2-7 it looks like the two subsystem EEPROM backups partitions live on the same block at adjacent addresses. On page 14, section 3.3 it actually states this in words "the EEE space is allocated starting at the beginning of the FlexRAM... up to programmed EEE size".
However, I am not sure whether that application note had the K60 in mind, since the K60FX512 reference manual (K60P144M150SF3RM ) shows this diagram on page 779, figure 30-32.
The above seems to imply that each of the two subsystems has its backup at the bottom of a 256K block, while that application note as I interpret it says that the EEE backup sections for both subsystems are adjacent and contiguous at the bottom of the combined 512K FlexNVM block, starting at 0x10000000 and continuing up to the total EEE backup size for both subsystems.
Which is correct?