Listen to music with outstanding guitar harmonies. Examples of songs with notable guitar harmonies include "Hotel California" by the Eagles, Boston's "More Than a Feeling" and Thin Lizzy's "The Boys are Back In Town." Don't listen to good examples of guitar harmonies with a view to emulating the actual guitar playing. Just listen to the way that the guitar parts harmonize.
Compose a song or piece of music on a guitar. Be aware of the need for a harmony part, so don't write anything too intricate. Make a simple recording of your composition.
Play the recording back and now work on the harmony parts for the guitar. You are really looking for a blend, so moving your fingers up and down the fret board, while playing the same notes as on the recording, will establish what harmonies work the best. Remember that these are meant to be notes that harmonize, so if just one note is discordant you'll have to change things. Mixing minors and majors is a good way of creating a contrast for a guitar harmony.
Record your guitar harmonies. Make a recording of each guitar harmony alongside your original recording. Listen to all the recordings and determine which is the best harmony. Keep the other recordings to consider how you can improve them.