All GUI appearances can be set by activating 'Edit mode'. Edit mode is turned on by pressing the 'Edit plot' toggle button in the toolbar. Once finished with editing turn back off edit mode.
Edit mode controls everything in the GUI: axis labels, object locations, object sizes, etc. For example, to change graph appearance (line width, line style, etc.) turn edit mode on. Then select your graph, right-click and choose your setting.
Note that in the current version of a|e the graphs will be restored to their original settings when the graph is updated. You can set graph colors permanently using the 'Set permanent graph color' button. You can set axis titles permanently using the 'Set