GSAK can automate the whole conversion process. You do not need to have OziExplorer running.
By selecting this option GSAK will:
1. Run the conversion.
2. Start up OziExplorer, if not already running.
3. Load up the waypoint file just generated.
It doesn't matter whether OziExplorer is running or not before you run the conversion. However, in order to start OziExplorer, GSAK needs to know where you installed it. If it is not installed in the default folder of C:\OziExplorer, GSAK prompts you for the correct folder. This only happens once, as the settings are saved for future use.