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 a model to the reference database by right clicking on the 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.