User data in the system EEPROM

The space taken by configuration depends on weather you're using compression or not.

If you don't use compression, it is fixed for a given FPGA model and you can find it in the device handbook (Table 9-3 in the Cyclone III handbook).

For the EP3C25, it's 5,800,000 bits. Which leaves you with about 60 Mbit left in the EPCS.

If you use compression, then it will change from design to design.

Those memory bits are dedicated to RAM.

The handbook is stating that there are 24,624 Logic Elements plus 66 M9K dedicated RAM blocks

66 * 9K => 608,256