CrystalMaker lets you display atom labels, which move as you move your structure. You can define the relative position of the labels (as well as the type of label), using the Labels group in the Model Inspector (View > Inspector > Model). You have various choices, either:
or:
Please note that these are global settings: you cannot select individual atom labels and move them by hand. (In any case, as soon as you move the structure, you would probably need to change label positions again!)
You can use the Lbl checkboxes in the Atoms Inspector to label atoms by site. Alternatively, you can select one or more atoms (e.g., by shift-clicking on them with the Arrow tool), and use the Selection Inspector to turn their labels on or off.
If you are preparing a diagram and want more control over labels and their positions, you may want to consider adding annotation objects. This lets you display textboxes - with or without frames, lines or arrows. Individual annotation objects can be moved, using the Arrow tool, and these objects float in a layer above the current structure. This makes them ideal for final-stage annotation.