Hello Sam, and welcome to the forum.
To select an ADC channel, and start a new conversion, the ADCSC1 register must be written, with the ADCH bits identifying the channel on which the conversion is to take place. Any write to this register will abort the current conversion, and commence a new conversion. Since you need to monitor nine channels, you should select single conversion mode.
I assume that the timer interrupt period is much greater than the ADC conversion period. For each interrupt it is not clear whether you require to initiate a single conversion on the next channel in the cycle, or perhaps you need to sample all channels in quick succession, within the timer interrupt period.
In the first case, the situation is very simple - you would not need to use the ADC interrupt. Within the timer ISR, read the result of the previous reading, increment the current channel, and initiate a new reading on the new channel.
For the second case, the situation is a little more complex. Within the timer interrupt, enable the ADC interrupt, and initiate a reading on the first channel. Then, when each ADC interrupt occurs, read the previous conversion result, increment the current channel, and initiate a new conversion. In the event that all nine conversions have been completed, disable further ADC interrupts, rather than start a conversion.
Regards,
Mac