Real time USB hi-speed Acquisition and plot with multiple timers

Hi, I'm developing a MATLAB-GUI to perform real time acquisition by an embedded acquisition board connected by hi-speed Usb based on pic32. I need to acquire the data at least every 5 ms, and refresh the plot at least every 0.5 sec. I tried to use two timers but they work only if I select a larger period for the acquisition (around 50ms). There is any way to perform the two tasks simultaneously? Is it possible to perform the two timer tasks on different cores of the PC sharing the data? Any suggestion would be appreciate