Filtering involves Digital Signal Processing. There is a useful online text about DSP which would give you a good introduction to filtering and also FFT and other aspects of DSP: http://www.dspguide.com/
Unfortunately, the Arduino forum is not the place to teach everything that you need to know and/or understand to enable you to implement an ECG platform.
Where are you getting the floating point numbers from in your message #9? How do you get -0.085, -0.080, etc.? The Physionet samples I've seen are 12-bit signed integers.
P.S. Why are you putting the samples in the EEPROM?
Pete