I am using the sd card as primary storage device and the flash memory to store the latest readings from the sensors.
I understand sensor data. I do not understand "primary storage" context. IF YOU have not resolved your inquiry, we can try to help but you are going to need to be more specific in what you wish to accomplish ...
This is a mandatory read for all Arduino newcomers:http://learn.adafruit.com/memories-of-an-arduino/arduino-memory-architecture
Unless your data acquisition lime is "long" then storing sensor data in EEPROM is unusual.
My earlier like is a serial-logger, that is absolutely everything written to the serial port is captured to the SD card. This can subsequently be read by any modern PC.