Datasets that are tagged for using an integral colormap will be colored with the discrete colormaps. You can set that in the header of the dataset with

3drefit -cmap INT_CMAP mydset.nii.gz

Alternatively, set the colormap to any colormap you like in the list (or make your own) by right-clicking on the color bar in the overlay panel and "choose colorscale". ROI_glasbey_nnn and ROI_nnn color maps work well for colors.

AFNI will send the colors as RGB values to suma when the two programs are talking to each other, so all changes will be reflected in suma. You may have to refresh the image with a small change in the threshold or some other minor adjustment. suma has a similar set of color maps available in the Cmp menu on the right of the surface object controller (available with ctrl-s from the main suma viewer window).

By default, the RGB values AFNI sends to suma are the locations where the surface nodes intersect the voxels. There is much more control with the Vol2Surf plugin if you want to explore more. The plugin gives similar control as the 3dVol2Surf program, just interactively inside AFNI. For example, you can compute the average or the mode (more appropriate for atlas ROIs) along the line segment connecting the pial and smoothwm surfaces.