Window

Keep running in background: When you first run OneCommander and close the Main Window, you're asked whether you want to leave OneCommander running in the background. This setting allows you to change your mind about what you want OneCommander to do under these circumstances.
Pressing Win+Alt+E from any program: If you're using Windows Virtual Desktops, you can choose whether Win+Alt+O (but not Ctrl+`) brings OneCommander to your current desktop, or changes Virtual Desktops to the one on which a OneCommander Main Window is currently open. If no Main Window is currently open, then whichever setting you choose, Win+Alt+E opens a OneCommander window in your current Virtual Desktop.
Use global hotkey Ctrl+' to show docked program window: Brings the window to the current screen, makes it full-width and at the bottom half of the screen. Pressing it a second time minimizes the window. Changing this setting requires a program restart.
This simply makes Ctrl+` do the same thing as Win+Alt+E, although it may conflict with other programs such as VS Code. 
If program has windows open, double-clicking its shortcut should: The shortcut referred to here is the one you double-click on to start the program, which may for example be in the Windows Start menu.
Show drives in sidebar: Shows or hides the Drives Group, giving you more space for Favorites Groups in the Sidebar.
Create default sidebar folders: This is your rescue button if you deleted the Default Favorites Group and subsequently wished you hadn't. 
Import Settings from V2: If you have OneCommander Version 2 on your computer and want to reuse its Favorites for Version 3, click here. No other settings can be imported from V2 because they're not compatible with V3, so you need to start afresh with your settings in V3.

Other

Command shell: Allows you to choose the Terminal that is opened by F10 (or Ctrl+F10 to open as Administrator).