Activating and deactivating Free running mode

Hi everyone, i have some problems with the free running mode of the ADC in Arduino MEGA ADK board, i'd like to use an ADC (for example ADC0 if i use the pin A0) in free running mode for a specific amount of time and then deactivate the free running mode because if i use an other ADC (for example the pin A1) with the instruction analogRead it doesn't works. Can i deabilitate the free running mode and use the analog pins with analogRead? Can anyone help me? Thank you.

I think what you want to do is possible, read section 26 of the datasheet: Mega2560 datasheet