Adding a margin moves the box wall out that distance from the bounding box of the geometry being translated. A feedline from the Virtuoso pin (Sonnet port) is added to the circuit and a reference plane is set for the length of the feedline.
For most devices, a good rule of thumb is to set the box size to three times the device circuit size. Since the inductor is in the center with a margin on either side, setting the margin to the width of the inductor provides the proper box size. Selecting the preset for an inductor set all of your margins to 100% of the circuit size, so the margin settings do not need to be changed. If you had needed to change them, you would have clicked on the Options button in the Analysis Box section to open the Analysis Box Options dialog box.