TMS320F280041C: MotorControl SDK Timer0 interrupt

Tool/software:

Greetings! I want to use Timer0(or Timer1 or Timer2) with MotorControl SDK. The problem is Timer0 interrupt flag is in the same group as ADC. So in the code the ADC interrupt use 

HAL_ackADCInt(halHandle, ADC_INT_NUMBER1);

which on my opinion will clear all the flags in group 1. Timer0 is in group 1. 

So what should I do in order to use both adc and timer0 interrupts?

Or should I use the timers without interrupts? Just checking their overflow flags?

Thanks!