I have a similar setup: 4 identical snowflakes, two off one output, two off a second output.
I created a custom model, and mapped the nodes (on the flake) to the model grid-layout in x-lights (starting at 1).
I then copy/paste this model in x-lights for my other flakes. Therefore, for each flake (in x-lights), the grid layout for each model starts at 1. HOWEVER, you set your "start-channel" independent for each model--depending on your set-up. This allows you to control each separately.
In my set-up, the "start-channel" for my second flake was simply "starts after snowflake one" (likewise for flake three and four).