The three Annotation-transfer methods described in this tutorial are
all complementary, and often any one of the three methods could be used
to do the same job with the same data-set. If you worked through
all exercises in this tutorial you will have seen that all three
methods were used to transfer annotations between related mitochondrial
genomes.
The tool you decide to use depends in part on whether you are working with closely or distantly related sequences and whether you have homologous annotated sequences suitable for transfer by alignment.
Be aware that generally the "Copy to..." method should only be used for wholesale transfer of annotations within an alignment if the sequences share homology across their entire length. Please consult the Geneious Manual Section 8.2.3 for further information on transfer of annotations.