The PSoC 3/5 Delta Sigma ADC is ALWAYS a differential ADC. When you select "Single Ended" operation, the tool simply connects the negative input to the internal Vss for you. If you route the the negative input to an external Vss, you are virtually doing the same thing, but with better accuracy since there will always be a slight difference between the internal Vssa and external Vssa. The only special case is the 0 to 2V range ( vss to Vref*2) where the negative input is connected to Vref. The ADC is still operating in a differential mode as Vref +/- Vref. Since in this case Vref is 1.024 volts you get 1.024 +/- 1.024 which is 0 to 2.048. To make the numbers come out right, the ADC's post processor adds the equivilent of 1.024 volts to the output reading.
So don't worry about mixing single and differential signals when the ADC option is set to "Differential" because the ADC really doesn't know the difference. Often I will use to single-ended muxes, one for the positive input and one for the negative input. They will often have a different number of inputs depending how many of the inputs or sensor share the same reference.
Hope that helps.
Thank you for the fast response. I need to mix differential and single ended inputs. I thought it would not be a problem but I needed your advice.