Im Using a Slightly older version im using 1.7.10 im trying to figure out how to automate some thermalilys from botania i tried to use a timer to block a buildcraft floodgate with a block of cobble but that didnt work because i couldnt get the times right if anyone can help me i would appreciate it also im not very good with redstone or mods but i will try my best
You cannot do it that way, since a Flood gate that cannot find a place to put a fluid will start "sleeping" for longer and longer and longer periods after each scan until it eventually finds a spot and resets again.
So once you remove the cobble block, the Flood Gate will be on a random, possible very long cooldown period.
If you apply a redstone signal directly to the floodgate, it will stop it from placing fluids AND reset the cooldown time back to zero. Release the signal then and it will start quickly filling in fluid.
So simple way is to use a NOT gate to invert the signal from a Timer. That way it it only places fluids at each of the Timers pulses.