If you add substrate on top of existing substrate does that bother the beneficial bacteria? I don't use a under gravel filter if that makes a difference with water moving through the gravel.
It shouldn't have any effect on the bacteria colony unless you add so much that water doesn't flow through the old substrate any more. Are you adding the same type substrate or something different? What do you have now?
As long as the tank has an established filter running, & you don't have an overstocked tank, you should be fine. If the tank is a newer setup, or is really stocked to the maximum, you could add half on one side, wait a week, and add the remainder to the other side.
I will be adding the same gravel but it will be over a gravel laterite mix since I pulled all the plants out to replace with new I just wanted to put gravel over it since alot of the laterite came up with the roots of the plants.