To make CE your default file manager, you go to:

• Control Panel
• Folder Options
• File Types
• Find the item that says "Folder"
• Click "Advanced"
• Click New, fill in the desired name
• For "Application used to perform action" you want to use CubicExplorer.exe
• Set this as the default action for Folder
• Save/Apply

To reverse these actions, just set open or explore as default actions.

(Thanks to nuKayos, thanhbv.)

An alternative solution (more precise) is using registry files (*.reg) like this:

Windows Registry Editor Version 5.00

[HKEY_CLASSES_ROOT\Folder\shell]
@="cubic"
[HKEY_CLASSES_ROOT\Folder\shell\cubic]
@="cubic"
[HKEY_CLASSES_ROOT\Folder\shell\cubic\command]
@="\"C:\\Program Files\\CubicExplorer\\CubicExplorer.exe\" /idlist,%I,%L"

[HKEY_CLASSES_ROOT\Drive\shell]
@="cubic"
[HKEY_CLASSES_ROOT\Drive\shell\cubic]
[HKEY_CLASSES_ROOT\Drive\shell\cubic\command]
@="\"C:\\Program Files\\CubicExplorer\\CubicExplorer.exe\" /idlist,%I,%L"

[HKEY_CLASSES_ROOT\Directory\shell]
@="cubic"
[HKEY_CLASSES_ROOT\Directory\shell\cubic]
[HKEY_CLASSES_ROOT\Directory\shell\cubic\command]
@="\"C:\\Program Files\\CubicExplorer\\CubicExplorer.exe\" /idlist,%I,%L"

Copy it in a text file with a "reg" extension and execute it for set CE as default file manager.

Windows Registry Editor Version 5.00

[HKEY_CLASSES_ROOT\Folder\shell]
@=""
[-HKEY_CLASSES_ROOT\Folder\shell\cubic]

[HKEY_CLASSES_ROOT\Drive\shell]
@=""
[-HKEY_CLASSES_ROOT\Drive\shell\cubic]

[HKEY_CLASSES_ROOT\Directory\shell]
@=""
[-HKEY_CLASSES_ROOT\Directory\shell\cubic]

Use it text for unset CE as default file manager

For more information about this alternative see relative forum post and another forum post.