If you want to use a custom image in place of a glyph styled within Glyph Designer, select the Atlas view and then drag the image you want to use onto the Glyph you want to replace. Doing this will cause the texture atlas to be updated to show the custom image in place of the standard glyph.
In the screen shot below the letter k has been replaced with a custom image.
When this font is exported the letter K will now be replaced with this custom image. The styling performed in Glyph Designer such as outlines and shadows will have no effect on glyphs which contain a custom image.
To clear a custom image, select the image you want to clear and make sure that the Metrics tab is selected in the right hand panel of the user interface. Within this panel is a button 'Reset Image'. Pressing this will cause the custom image to be removed and the generated image using the defined styling to be used in its place.
When using custom images it is often necessary to change the alignment of the image to make sure that it lines up correctly with other glyphs in your font. Details on how to do this can be found here.