I store water in 2 liter soda bottles, & have had it keep well for 6 months to 1 year. We "rotate" the water when drought conditions do not allow watering of the garden in July or August, & guess where we dump the "old" water??
I think storing some "canned" water is a good idea, because you never know when some sterilized water will come in handy. Using bottles to "fill" the empty spots in the canner seems like an intelligent way to do it to me, especially with re-used lids.