The correct phrase is "Once in a while" (to separate words). 

As "awhile" is an adverb, it *wouldn't* make sense to say "Once in awhile".
See V0ight's comment:
> Replace 'awhile' with any other adverb, like 'rarely' or 'seldom' and you'll see it makes no sense. 'Once in rarely'? 'Once in seldom'?