Here is my model...
Ideally I'd have 9 strings of 19 nodes I suppose and then all the channels would align.
However in my case I don't have the same number of nodes on each branch.
1-22
2-21
3-21
4-19
5-18
6-19
7-18
8-18
9-20
The above table is really what I have on the tree.
Can I change the individual start channels and keep it at 20 nodes,or does it really not matter (assuming I don't over lap channels beyond the 176 nodes I have)...if that makes sense? BTW It's early and no coffee so I can see how this post is confusing 
I would create a "custom" model in Nutcracker for the actual number of nodes you have and put in the correct starting pixelnet ch#.
You might create this as a grid with a certain x and y size ... then click on the grid button and you enter in the nodes in whatever physical order you used when installing them onto the tree.
I would do a custom model width of 9 and height of 22 (your max used in any of the 9).
Then go in literally type in the first column (A) the nodes used bottom to top (?) 1,2,3,4,5,6,7....22 (22 total) and then go into the next column (B) and type in top to bottom (if thats how you wired it once you hit the top) .... 23,24,25,,,43 (21 total) ... and keep doing this this you get the nodes shown in the custom model grid.
This example assume you went up for the first 22 nodes, then down the next 21 and then back up for 21 ... and so on per your specs.