While sitting very slouched on my couch is my preferred method of playing, I did play many segments of Skyward Sword lying on the floor (because my shaggy carpet really is that comfortable) without much issue. Some sword fights pretty much beg for you to at least sit up, and when flying, I sometimes found it awkward to dive when lying on the floor, though if you're on a bed, I imagine this will be less of an issue. Holding the Wii 'Mote vertically isn't that big of a deal when lying down, as I did it without issue.
Just remember, when playing Skyward Sword, Down on the D-Pad is your best friend, especially if you'll be playing in an unconventional position (such as really, really slouched, or lying down).