The best way to measure  patch electrode series resistance (Rs) and synaptic peak amplitude (PkAmp) online is to measure Rs from the unfilterd trace, and PkAmp from the low-pass filtered trace. Rs measurement is made from the capacitative peak transient from the unfiltered trace so as to not attenuate the transient peak (20 KHz sampling, 10 KHz external filtering). The PkAmp measurement of the synaptic currents is made from filtered trace so as to not measure the superimposed excess noise (20 KHz sampling, 10 KHz external filtering, 500 Hz internal filtering). As shown in the figure below, the Rs and Rm measurements were made from the gray 10 KHz unfiltered trace, whereas the PkAmp of the EPSCs were measured from the blue internal 500 Hz filtered trace.

For more information see Section 4.11.11 in the on-line WinLTP Manual.