My preference is to store the whisky in its bottle, but use the decanter when having a party or just a few guests over. It really is a nice touch. Also, properly storing whisky means keeping it out of sunlight and in cool temps - so even if you kept it in a decanter, you wouldn't want to leave it out for an extended period of time anyway. Best to keep in a cool, dark place -and- if the bottle came with a box, I would even go so far as to keeping it in it when not using (I think that's what you're supposed to do).
One more thing, decanter glass tops may not fit properly which could cause evaporation. Don't you think the angels have had enough of their share?!