My emperor 400 puts the intake strainer at about halfway down the back wall of the tank. Should I use the extension and adapter included, cut them to fit, and put the main intake at the bottom with the extension strainer in the middle? Or will it be fine like it is? Thanks!

With my Emperor 400's I wanted the strainer basket down close to the bottom, but it was too long with the extender tube so I cut a piece off, about two inches long, and everything fit perfect.

Hope this helps!

Do they work better with the intake closer to the bottom of the tank?

In general, yes.

Thanks! I will play with that the next time I have a waterchange.