Do you have ball valves on the two inlet pipes to your pump to regulate how much each one (skimmer and bottom drain) is pulling? I have seen some schematics for pond plumbing drawn that way.I have a garden pond with goldfish and a few orfes. I agree that a bottom drain is a personal choice, as is everything else pond related. There is no right or wrong way as long as it works for you.
The bottom drain pipe goes to the pump which is in our garage with the pressure filter. There is a leaf basket at the front of the pump housing that collects any debris. But honestly there isn't much.
I clean the leaf basket every couple of weeks or so and most of what is in there is a little algae and a few snails. In fall there may be a few leaves, but the skimmer takes care of most of those.
The skimmer pipe joins up with the pipe from the bottom drain just in front of the pump.
I hope that helps.
I've got a ton of trees around, and some new planted Maples that are close will make more leaves as they get older. On a positive note though, they will provide shade in the future. I definitely plan on buying an EXTRA large skimmer.