You are right, without bootmii as boot2, you shouldn't mess too much with the original nand contents and system menu.
There is debug output coming from uneek, but you need an usb gecko to capture it and view it on your pc.
I am working on a system to regain full sd access in sneek and full usb access in uneek. To use it, you need a different s(u)neek version and the homebrew needs some small modifications as well. Those are pretty simple to implement, and the homebrew stays compatible when it's used on a real nand.
In the tutorial section, you can find my article that describes the use of sneek in a sd-only setup. It might contain usefull information for a more generic setup as well.
Do you have a specific purpose for your sneek setup, like playing a game backup that doesn't work with the usb loaders, or playing some VC - Wiiware? It's also possible that you are trying to create a more brick proof system on your wii.