there is a return to channel feature in configurable usb-loader, wiiflow, joyflow and probably also usb-loader gx. What this does is it patches the wii home menu, so that when you're in a game and select "Wii Menu" it actually starts the channel you chose instead of the wii menu.
So basically all you need to do is set your usb-loader "return to" settings to load a usb-loader forwarder channel, then everytime you start a game from the usb-loader and select "Wii Menu" from the wii home menu it will take you back to your usb-loader instead of the main wii menu.
To do this, you must have a forwarder channel installed and you have to know it's title ID. You probably already have one installed from when you used ModMii (it should look like a spinning hard drive). If so, the title ID for this channel is "IDCL". If you don't have a forwarder channel installed, install one (u can use ModMii's channel or if you find one you like somewhere else that's fine too, just make sure to use the correct title ID in the following steps).
then in configurable usb-loader's config.txt file (IIRC typically found in the USB:\usb-loader\ folder) add the following line:
Note you can also use the configurator for configurable usb loader (saved in the same folder) to help you further modify your config files if you want to customize your cfg usbloader further.
And that's it, now when you launch games from configurable, you can select the "Wii Menu" from the in-game wii home menu and it will take you back to configurable usb-loader.
setting up the return-to-channel feature is even easier in joyflow and wiiflow, you can actually do it on your Wii and it will let you pick from a list of your installed title-IDs\channels.
About your cover issue, I had a similar problem once and it turned out it was because of a lack of free space on the sd card. Also make sure if you have a lock switch on the sd card that it is unlocked (otherwise it wont be able to write to the card).