I need more detail to understand this question. What are you trying to measure? Are you making two patches on one cell? It is not expected that two electrodes should affect signal-to-noise, so I wonder what brought the possibility up.
I agree that that position of two electrodes should not affect signal-to-noise in configuration of two isolated circuits either when recorded from the same cell, two different cells or in solution. Increase in noise with different electrode position is likely artifact of electromagnetic interference whereas the decrease of the signal might be due to bleed between circuits.