Welcome in the forum, Karthik!
Sadly the PSoC5 has got only 4 OpAmps which will be short of 1 OpAmp when using the 3-OpAmp instrumentation amplifier.
So I would suggest you to use 2 external IAs which usually have got a better characteristic than the PSoC internal.
Fine Bob, then, can i use "Two Opamp Topology" to acquire signals from 2 channels ?
Signal quality depends on your gain. most common error made in this context is:
All signals have to be in the range >= GND and <= VDDA. You might need a level-shifter (R-ladder) for the inputs.
If you are going to feed the signal into the ADC anyway, you are better off to use the two opamp method and measure it differentially anyway. Also, you can mux the inputs of the opamps so you can measure two or more differential channels.