Right click on Model databases, you can import a metabolic model in SBML/spreadsheet format as described in Metabolic Models.
You can directly edit/update the content of the imported model.
Right click on Reference databases, you can import a reference database provided in Reference Databases to create your own reference database.
You can add the information about metabolites and reactions described in your model to the reference database by right clicking on a metabolic model.
A draft reconstruction can be generated by mapping a blank reconstruction outputed by GBKParser, containing gene information only, to a reference reconstruction.
GEMsME will extract the reactions whose associated orthologous genes can be mapped to the reference reconstruction once the list of orthologous-gene pairs is available.