I am led to believe that a planted bog will act to benefit a pond's water quality. Then In planning a bog addition to an existing pond, where water will pass through a rocky berm, shouldn't the flow be towards the pond?

Everything that I read suggests the opposite.

Most shallow attached plant areas (vegetative filters, bogs (not true bogs which are acidic), etc.) are upstream of the main pond. They could be below the pond but then fish would most likely end up down there. The attached planted ponds are normally above the main pond to keep the fish out. Also, since they are usually a smaller volume, it makes more sense as far as pumps and flows go. For example, if the bog were at a lower grade, and the pump failed, excess water might flow down there and lower the main pond's water level. In a pond setup with multiple ponds/levels, the largest volume of water should be at the lowest level or the most downstream.

Sometimes, people create bog ponds at the overflow of the pond. They are not attached to the main pond in that their water is not circulated back up into the main pond. That means the bogs can be real bogs that are very acidic. They would only flood when the pond overflows.

Re-thinking the upstream bog, would this work if the bog plants were planted in soil/peat instead of pots? Also, I would like to add pebbles to the surface to keep things in place.

If you plant a true bog pond with soil and peat and connect it to a traditional pond, it will lower the pH of that pond as well. If you use a substrate of just dirt and cover that with pea gravel, it should be fine for a few years but will need to be changed out every two or three years. Such ponds are hard to clean and start to stink in a few years. If you use just gravel (no dirt), it will last much longer. Many pond plants will do fine in just gravel but not the true bog plants. Did you want true bog plants or just marginal pond plants in there? Pots allow more control whereas filling the pond with dirt and gravel is more natural. It's your choice.