I think from the way you are explaining it I have a very similar set up. On the left side of my tank I have attached to the back an Aqua C remora, and just to the right of that the intake for my Eheim canister, then to the right of that a little the spray bar output. I have no problem what so ever with bubbles. Now, I have had it set up for over a year, but honestly I do not ever remember really having a bubble problem. I have noticed that when the water level gets low, and it has a longer distance to fall to the tank, there are more bubbles. Also you could try spacing things out a bit, if one is spitting out bubbles and the other is sucking them up, they could just keep going.
Are you saying that your intake for your canister is putting out bubbles, or your return? I am not certain how your intake could be putting out bubbles? So assume you are talking about your return, is there any chance that air is getting into the lin somewhere. I notice that with mine if i jiggle the return hose a bit, then the spray bar spits out a ton of bubbles. I know that this is because I have a connection that is sucking in some air.
I don't know if that helps or not, but hopefully it does.
Mit freundlichen Grüßen