The analog ground (VSSA) is as important as any of the signals you are measuring. The trace between the PSoC VSSA pin and the system ground must be as short and low impedance as possible. Sharing this path with any component that uses even a few hundred micro-amperes can cause problems when measuring sub-milli-volt signals. An offset can translate into a measurement offset when using single-ended measurements. It is better to use the same analog ground for the opamp circuit. Kindly see Shared Return paths in the following document: PSoC® 3, PSoC 4, and PSoC 5LP Mixed-Signal Circuit Board Layout Considerations.
Regarding ADC you can have multiple channels using 12 bit resolution. You can use the Sequencing SAR component as it will take care of the switching between channels.