You have it all right. For every parcellation, there are several versions of the niml.dsets, and all of them should be equivalent for processing. For visualization, there are some differences:

1. surfatlas directory have no colormaps assigned, so in suma you would assign a color map yourself with the Cmp button
2. surfsets has two versions - lbl.niml.dset and cmap.lbl.niml.dset. The former has the color map from the original Schaefer-Yeo colors. The latter uses the Glasbey1024 colormap. The Glasbey colormap helps to discriminate colors across regions. The original SY colors tries to use very similar colors within broad regions of the brain.