I use usbloader gx, and i like it. Configurable usb loader, and wiiflow are also good. If you have the game on a harddrive, you wont need to use the disk.
For your also, im not really sure. I format my drive to WBFS, which windows cannot read, you have to use a special program to load games to it. But i know its also possible to use fat32, and maybe ntsf(not sure about this one) which windows can read, but you have to use a program to convert the iso files into a different format. You'll have to look up some guides for it, or maybe someone will direct you to some. Again, as i dont use this method, im not too familiar with it.