Hi, 

The water sitting for a few days is fine. You may want to have some type of screen system to prevent animals from falling in or mosquitos from breeding, also to keep out leaf litter debris that might fall in there and would decompose and cause bacterial growth.

You can review this study done by Rutgers about rain barrel and cistern collection systems and runoff from roofs. Some roofing material can contain certain heavy metals and carcinogenic material. The study showed that the levels tested were deemed safe by EPA standards but due to the fecal cauliform and bacterial levels (E.coli) it was best to just not splash the foliage of the plants when watering. However, you may not want to risk it, it would be a personal choice.  Personally I would not water edible plants with water collected from a roof or driveway and would rather stick with hose water or collected rain water just from an open source. You also have the option of treating it with some chlorine if you are concerned ( just make sure it is the appropriate amount). Roof water that is collected could still be used for trees or ornamental plants, for washing cars, for power outages etc. 

In some spare time you may want to watch this informative webinar (about an hour long - or skim through it) on rain barrels which answers some more questions about harvesting water and use in different ways around your landscape. 

Let us know if you have further questions about this. -Emily