The Automatic Restriction Enzyme Analysis tool that is displayed on the sequence in the Map tab is very powerful. It automatically displays a custom set of restriction enzyme recognition sites on every sequence that you open. Unique recognition sites are displayed in red and sites with two or more cut locations are displayed in blue. Those sites also show the total number of cut locations of that recognition site.
To select every site of a single enzyme just double click on a single site and every other site will also be selected. Additionally the Graphics Palette will now show those enzyme sites in the Results tree view.
To change the Automatic RE Analysis options open MACVECTOR > PREFERENCES and switch to the MAP tab. Read more about restriction mapping.