I think the main reason for having in and out on the same side of the tank is to help bring detritus back to the filter. Whether you are using a spray bar or a jet output it will most likely shoot across the top of the tank, it hits the far side of the tank and curves downward to sweep across the substrate (picking up gunk) and bringing that gunk to the filter.
I think the way you have it set now you may not be getting that water motion over the substrate.
this does seem to be the case. I paid closer attention to the flow in my tank when I got home last night. Even though there was a pretty steady flow throughout the tank, when I moved the intake to the same side as the outflow, the flow along my substrate seemed to increase pretty noticeably.
If you find that you need a powerhead, go for a koralia nano. I run a nano 240 in my 46g bow front and it helps bring the flow back across keeping everything laminar. The bonus is that the nano agitates the surface a bit for me. I also have and tried a nano 425 but it was a bit too strong for my tank.
thanks bsantucci, koralia is actually what i was looking at and seem to have a great reputation on here, they have been recommended to me before. thanks for all your input.
Part of the benefits of running a canister filter is that you can customize so much to the needs of your particular tank.
Position them however works best with your particular hardscape, softscape, and fish.
this is my first time using a canister filter and I must say i'll never go back to a HOB.
I have an Eheim 2217 with intake and outflow at opposite ends of a 55 gallon (4 foot) tank. I did not know that having the intake and outflow on the same side is the "correct" setup. I don't think I have any dead spots. All my plants sway gently, and the CO2 bubbles coming out of my spraybar disperse all through the tank. I have the holes on my spraybar aimed slightly downward so that the CO2 bubbles get blown through all levels instead of just staying near the top. Maybe someday I'll move the intake and outflow to the same side to see what difference it makes.
I tried switching it up last night and even though it seemed that i was obtaining pretty good flow with the pipes on opposite ends of the tank, when I put them on the same side it definitely seemed to increase flow near the substrate.
In all honesty, I tried to make the perfect set up when purchasing equipment for this tank. Many people seem to use eheim canister filters on these 12g long tanks so thats what I decided to go with. But I can't for the life of me figure out why so many people have flow issues on these tanks. This canister filter does and awesome job without need for a powerhead IMO

roud: but i guess i'll give it a month and see how everything turns out before i make any more assumptions.
thanks for all the input everyone. much appreciated.