The main reason for the seas to be a bit calmer at night is mostly due to wind. The sun powers the wind, which blows across the water, creating its waves and its own current. This is why at night, the surface water seems to be calmer due to less wind. But beneath the waves, the worlds currents usually stay the same.
From my time diving in Hawaii, the current is quite strong compared to what I have reproduced in my little environment. The whole water column moves as a whole, rather than the streams created by power heads or closed loops. As some have mentioned, creating random currents is the key.
Live rock in your tank should provide the necessary cover for your fish to take a break. But if you wanted to replicate nature a little better, slow your flow over the surface of the water. It will also slow the currents lower in your tank just a little but, but not too much to need to worry about detrious settling.
And remember, different corals thrive in different locations(surf, lagoons, deep water, etc.). These areas usually provide the same type of environment day after day. So coral selection along with flow of your tank, lighting, etc., are very important in order to mimic their natural settings.
Ocean life was created in order to keep things in balance, not to look nice. So putting two colonies in your tank, that normally are in different aquatic environments, will allow one to thrive while the other hardly does well at all. Even though they both would look great in your tank, they aren't meant to both be there together. So much consideration needs to be taken with the type of coral you can keep with the flow your tank provides.