When a Chart opens, Voyager examines whether it's an IFR or VFR flight to determine which theme (Chart settings) to use. If no flight plan is involved, it uses your default preference for IFR vs. VFR (Tools/Options/Plan Type). You can tell Voyager which theme to use for IFR and VFR modes individually with the Default VFR theme and Default IFR theme drop-downs.
Additionally, you can customize each theme or add new ones. Simply set the Chart settings as you like them select Edit from the Themes menu and click Set.