How do I arrange my data to predict 6 weeks of daily sales
I guess it depends on exactly what you want - do you want a forecast per store? If so you would need to leave the data set aggregated only to a store level. If not, and you want the overall sales by day, then you are OK to leave it aggregated.

Another consideration is whether there are many store-level features e.g. location, weather, local demographics. These features may be useful for the model to learn from and would lose resolution if store level data is aggregated, therefore leaving it un-aggregated would be better. The counter point to this is whether you have enough data for each store to learn representative trends! So it does get kind of circular and depends on the size of your data set.