How do you handle multiple TPanel's at design-time?

If only one panel is visible at a time, then you might want to use a TPageControl to organize things. You can click the tabs to select which one to work on at design time, and then hide the tabs at run time, or hide the tabs all the time and select pages by setting the ActivePage property.

Use the Structure Pane to find the one you want, and then bring it to the front.

_{(source: embarcadero.com)}

(But don't follow Embarcadero's example above; give your controls meaningful names so your controls are easier to tell apart.)

If the panels are stacked, you can reorder them by right-clicking on one and choosing Control->Bring to Front or Control->Send to Back from the context menu.