BLDC 3 phases low side current sensing
You do need to set an ISR for each analog input. The correct timing sequence is subject to PWM pulse driving sequence, amplifier settling time, analog input settling time, sample/hold settling time,...
You may find some articles from STM32, TI, Freescale, using SPWM and similar modulation, when exactly you should take samples, also formulas for computing phase currents.
TI example FOC - (not six step BLDC !!)
Freescale example FOC 
STM32 example FOC 

Microchip FOC phase currents measurement

If you have a six step commutation, then only one upper and one lower transistor is conducting. 1st ISR is starts when both transistors are on, this enables 2nd ISR a delay time, so that current and amplifier have settled, at 2nd ISR you do take a sample from corresponding phase ADC, this enables the 3rd ISR - conversion end. At 3rd ISR the conversion is finished and you store the value.