It is frequently necessary to change the order in which files appear in a layer. This could be used to control the order of menu items in a menu, for example.
Right-click on any file or folder inside the layer. If you wish to set the relative order of files defined by your layer within one folder, click Reorder... on the folder or Move Up or Move Down on a file to change this order. You will see the layer XML update with relative ordering constraints.
It is also common to request that a file provided by your layer be installed in some position relative to existing files in the IDE (in the matching folder). To fix your file in this way, right click it and select Install... and choose the desired position of your file in the containing folder.