No, I do not open the inner bag before sealing it. The point is just to contain any insects within the Foodsaver bag and to prevent moisture from causing the cereal to spoil quicker. Leaving the original packaging bag still sealed causes no detriment to the vacuum sealing with the vacuum sealer.
I know what you mean about the flour. I recently opened the last bag of bread flour purchased in Panama
in March 2008. Still fine. However, I do not fully vacuum seal all-purpose flour because it clumps if sealed hard-as-a-rock.
Bread flour does not clump.