Sounds to me like you do not know well how to use timers.
Use interrupt on timer overflow. In this interrupt function set a int flag = 1.
In your main program code ... whatever it is just use if condition if in a loop... if flag is 1 then "do something" do something is done then flag is 0. next time loop checks the statement it will just will pass "do something" part and thats all you need.
To do the bilking part you need to turn PWM on or off in "do something" if flag is 1.