I've fiddled and played with all types of skimmers until the sun came up, just because I'm facinated by these things and how they have dramatically helped the life of my tanks. I've also played with many configs of my Remora and took really close notes of what worked in didn't.
There's a misconception that putting a filter of any type on a tank will insure 100% of the water in the tank will go through the filter just because you have a big pump on it. Such is not true. *Any* filter that has the input in relative close proximity to the output is going to lose efficiency because a lot of the water just keeps going back through the filter.
With a big back filter like a Emperor 400 it's not quite a problem. The Emperor dumps a huge volume of water back into the tank and basically uses a brute force approach to water movement. The Remora however moves a trickle of water compared to the 400, and hence can't move the mass of water on it's own. So, a large percentage of freshly skimmed water just gets skimmed over and over.
Ideally any skimmer does best in a place where the water entering comes from the opposite side of the tank from where the water exits the skimmer. This insures that the skimmer is getting a constant supply of fresh water.
However, with a hang on style skimmer this isn't always practical unless you feel like sticking a plastic pipe on your powerhead and extending it to the opposite side of the tank, which is kind of ugly. My compromise was to put the Remora's powerhead literally inside my Aquaclear 500 filter box sitting on the opposite side of my tank, and run the plumbing from there. It worked, but was a real pain to do.
If your tank were *my* tank and wanted to keep things simple, I'd put the Emperor 400 smack dab in the middle of the tank and park the Remora immediatley on the right side of it. This way the Remora is sitting close to the draft of the 400 much like sitting behind a semi on the highway to 'ride his draft and steal the current. Sticking a Remora at the end of a tank is the *worst* place you want it unless you can figure out a way to feed it water directly from the other side.
I also agree that surface skimming is important, but an Emperor 400 renders it moot is an average size tank. The Emperor is literally dumping over a ton of water per hour onto the the surface of the water, and hence the water column in all but the largest tanks is going to be pretty even.