I think it should work - in a recent project I had 2 ISRr trigger by timer components (one with 10Hz and the other one with 1000Hz). What do you want to do exactly?
There is no such restriction. As a rule of thumb:
Declare your interrupt handlers with CY_ISR_PROTO() and define them with CY_ISR() macros. Both explained in short in the System Reference Guide (Help -> Documentation -> System Reference ->)
Use isr_StartEx() to tell which handler will use which isr.
Keep the handlers short, no output to LCD, do not wait for anything.
Since you are going to program a closed loop (PID) you'll need a (relatively) constant time-base (20 to 50 ms) get the 3 values of the on-board accellerometer and call your PID-function.