ModMii can walk u through most of the process. Start ModMii, from the main menu type "S", then type "3" to set up s/uneek and an emulated nand, on the next menu I recommend you choose "UD" Uneek+DI, but read the explanation of each of them to determine which is best for you, then answer the rest of the prompts and let ModMii do it's thing. Be sure to read the quick tips that are displayed during the install.
If you choose sneek+di or uneek+di, u will also need at least one game saved to your hard drive in sneek format (ModMii can do that for u too, from the main menu type "S" then "4")
When you're done, plug the sd card and/or hard drive in your wii. If u have bootmii @ boot2, s/uneek will load automatically when you power on the Wii. If you only have bootmii installed as IOS, u will need to launch bootmii @ IOS from the HBC or priiloader. When s/uneek is loading for the first time, it expands its files on the emulated nand, so it may take some time (5-10 minutes) before you reach the emulated nand system menu. The next time it loads it will be much much faster.
I realize you are asking about mighty channels, not s/uneek, but they are so closely related that this route makes sense. Anyways, you should launch s/uneek at least once in order to expand your emulated nand otherwise it may not operate properly in mighty channels.
So now u are almost done, stay with me!
All u need to do now is install channels to your emu nand. So plug the sd card or HDD back into windows, download showmiiwads (google for it). Start showmiiwads (accept the risks in the disclaimer), build the common key (tools-->create common key), change the nand backup path to wherever your emulated nand is which should be your usb if u chose uneek or sd card if u chose sneek (options-->change nand backup path), then go to view-->showmiinand. Then just drag and drop whatever wads/games u want on your emulated nand, and at the bottom click the 'install' text button. Wait for it to finish. Now the next time u start s/uneek u will be able to play those games off your emulated nand.
Now, this is the last step and the easiest. Download mighty channels, save it to your sd card or usb, then start the HBC from your real nand (so not from inside s/uneek) and load mighty channels. There u will see all the games u installed to your emu nand from the previous step.
FYI, best compatability for mighty channels is with cIOS249 d2x v3 base 56, which can only be downloaded from ModMii (download page 4).
I really spelled out every single little step. So while the above text might seem daunting, I probably could've explained it with less words but I wanted to make sure I covered everything.