The boot.dol allows an application on Homebrew to launch. It allows you to run the modification when you select it.
There should be three files to allow the app to run (Not the cIOS) (Just the installer for it.)
Those files are a
.png (Renders Photo on HBC to show app picture/banner.)
.dol (Allows you to boot into the application.)
.xml (I'm guessing data.)
Without those files on the app's folder with the sub folder that goes into it (In this case cIOS d2x installer.) They should be in a named folder for it (So the directory should be SD:/apps/(Name of cIOS d2x installer.)
Also I'm just talking about myself... I know embarcing, happens when I talk in discussions sometimes, and no those files are just to launch the app, and allow it to function. You don't need the files present once you install the cIOS because it will already be on the system NAND.
Also the WAD Files (AKA) cIOS should not be on the root of the SD Card. The only time they should be on the root is if an app searches for the wad directly on the SD Card, (An example would be Priiloader hash/hacks.ini file.) The WAD's (aka cIOS Files.) (In this case the ones you installed.) Are required for the system to allow USB Loader GX to work correctly with USB Support so therefore they must be present on the Wii NAND since it can't search, and function on the SD Card at the same time (If that makes any sense.)
The D-Pad is the controller navigation (Left, Right, Up, Down.) It controllers where you move on the screen.
So your saying you installed the cIOS File, and it is installed perfectly. But the Wii remotes turn off ocasionally (or on boot.) Try
@Cyan 's method, is your Wii Remote turning off with any other app's, or is it just this particular one in general? If so it can't be a problem with the Wii Remote, it's a problem with the app on HBC not rendering your Wiimote properly. That's why I suggested to use a regular Wii remote to test if the mod can identify it.
Also it's no problem. We're all trying to help you figure this out.