No, your data will automatically be transferred to the new version. You will also be asked if you want to keep a backup for the previous version the first time you open the new version.
However, we do suggest that you take a separate backup of all of your data in Geneious as well before upgrading. To do this use the option File->Back Up Data.
If for some reason Geneious cannot find your data folder from the previous version when the opening the new version for the first time, you can load the previous version's data by going to Tools->Preferences->General, and setting the data storage location to the previous data folder you were using.