^{Menu: Settings → Window Settings → Save Window Positions and Size}

If you click on this menu item a check appears next to Save Window Position and Size while activating the option, while deactivating the option the check disappears.

If the option is active Emu64 will save all sizes and positions of all open windows (C64 screen, floppy window, and so on) on shutting down the program. When you start Emu64 again the C64 screen is positioned and sized just like it was before you closed Emu64. The opened windows are not reopened on startup, but once you open them up manually they have the same size as before and are on the very same position as they were before.