Timer 0 is use'd by the arduino core libraries for functions like millis(). It is best left alone. Leaving timer1 and 3 are available for general use. Both 1 and 3 have well established libraries, for simple implementation, without the need to know the mechanics under the hood, about the registers and such.
You can find links and general explanations at timer1. I always recommend the github versions.
And if you are still wanting to know the details the source is quite readible.
Note you don't need 3 timers to read 3 sensors. One timer on a multiple of the the 3, should suffice which can then implement a statemachine to sample at the correct periods.