The 3dcalc help example 6 offers some guidance on composing a dataset with binary choices for conditions. Overlaps are allowed and shown in different colors. I'm guessing for this OP the Instacalc/3dcalc solution would be sufficient, but there are a couple other ways afni can show multiple datasets.

The "Show Atlas Colors" menu allows a single atlas dataset to define the color shown where it is non-zero and a color has been selected manually for each integer value in the dataset. A dataset would have to be "atlasized" first to make this useable and AFNI_ATLAS_COLORS would have to point to this new atlas. Yes, it's awkward, but it does allow a dataset with selected regions in solid colors to be shown over another dataset. The Overlay panel allows the user to toggle the display of the atlas overlay.

Another way is to use 3dThreetoRGB and compose a single dataset with three components. Each component is assigned a value of red, green or blue. This method is convenient for comparing up to 3 regions with the first region assigned a color of red, the second green and the third blue. Here is an example with the output of the top 3 clusters by size from a 3dclust/Interactive Clusterize mask dataset.

3dThreetoRGB -prefix Clust_rgb -scale 255 Clust_mask+orig'<1>' Clust_mask+orig'<2>' Clust_mask+orig'<3>'

That example doesn't have any overlap, but if it did the overlap would be the combination of red, green and blue (all overlapping would be white). The RGB value dataset that results can be shown in the existing AFNI underlay or overlay. The overlay allows opacity control even for RGB datasets.