There really isn't a good way to have multiple overlays in the AFNI GUI.
You could multiple the stats map DSET_STATS by the region map DSET_ROI, adn show that:
3dcalc -a DSET_STATS -b DSET_ROI -expr 'step(b)*a' -prefix DSET_STATS_IN_ROI
... and then use DSET_STATS_IN_ROI as the overlay.
A somewhat cheating method might be to concatenate the stats volume and the ROI one, and use the ROI one as the alpha map
+ Make an "elevated ROI" map, which is 2 in your ROI, and 1 elsewhere that you want to see stuff (and maybe 0 outside that); for example, here is one that is 2 in the ROI and 1 elsewhere:
3dcalc -a MMM1.nii.gz -expr 'step(a)+1' -prefix DSET_ROI_ELEVATED.nii.gz
+ Concatenate your desired stats volume and the 'elevated ROI map':
3dTcat -overwrite -prefix dset_stat_and_mask.nii.gz stats.FT+tlrc.'[2]' DSET_ROI_ELEVATED.nii.gz
View it with @chauffeur_afni now, thresholding the elevated ROI map at, say, 1.5:
@chauffeur_afni -echo \
-ulay MNI152_2009_template_SSW.nii.gz \
-olay dset_stat_and_mask.nii.gz \
-box_focus_slices AMASK_FOCUS_ULAY \
-func_range 3 \
-cbar Reds_and_Blues_Inv \
-thr_olay 1.5 \
-olay_alpha Yes \
-olay_boxed Yes \
-set_subbricks 0 0 1 \
-opacity 6 \
-prefix IMG_ROI_STAT \
-set_xhairs OFF \
-montx 3 -monty 3 \
-label_mode 1 -label_size 4
--pt
