You mean you install the game to the Wii, not extract it again?

I'll tell you how i do it.

I extract it to my SD card. Plug that into my PC and just edit it on the SD card (i don't mess about moving the save file or anything). Once I'm done i save and then put my SD card back into the Wii.

Now go the the save installer and load that up. Follow the instructions and when you're game comes on all the changes you've made should be there.