The embedded PDF viewer has a very powerful tool, the Ruler. It lets you measure lengths and generate LilyPond code to move around object.
To use this tool, select its button, and click and drag the mouse. If you clicked on a point-and-click target (like a notehead), it's graphic is also shown while dragging, to help visual positioning. After you release the mouse button, a dialog box appears, where you can drive the code generated from this measuring. You have the following options:
Here you can select the staff size in which the length is calculated. LilyPondTool tries to guess this, but it may fail, so make sure that it is correct.
These are the measure lengths.
If you check this checkbox, an \override command will be generated if you select the property.
If you check this, LilyPondTool will look for the last used override (relative to the moved grob's location in the file), and overwrite that with the new values. If the is checked, it won't override, but add the offset to the existing value.
If this is checked, the existing \override will not be overridden, but the new offset added to the existing offset. This must be used, when you've already adjusted some lengths, but you are not content with the result and want further offset.
Often LilyPond wants the length to set with different sign, this check will invert the sign.
Here you can select, which axis to use, X (horizontal), Y (vertical) or both. The latter is enabled only for those properties which get a pair as value.