You may have better luck getting help if you post the file. The method you are using works best in large open areas with relative uniform slopes. It is not going to work well if you are crossing walls, channels or any major surface breakline areas unless both surfaces share a common closed boundary. The boundary must be identical at every vertex x,y and z.
OK, I'm familiar with streams, just not the technical terminology. I think you've explained it pretty well.
I think you'll have to get into some pretty detailed design. I would use feature lines to define the top of each basin (sort of in a circle for each one) and another one for the bottom. Then another two or three running down the length, crossing each basin to define your thalweg. Another couple of feature lines running down each sidie to define the edges.
You could start off by using the elevations from surface command to pick up the existing elevations at the points where you're tying into the existing stream. Then edit the middle parts. The elevation editor shows you the % grade of each segment of the feature line.
You could add this to the rest of your proposed surface, or build it seperately as a 'Proposed Streambed" surface. Then paste that in to your combined surface at the end.
Credit where credit is due! Give kudos or accept as solution whenever you can.