If your soil is well drained your daffodils should tolerate watering, as long as you choose annuals that don't require a whole lot of water. As a rule, begonias don't do well here so I don't feel qualified to speak to that. Just keep in mind that daffodils really do prefer the soil to be on the dry side during the summer. Just how dry it needs to be will depend on the varieties you planted. I know that's not alot of help, but there it is.

By the way, there are a number of annuals that deer don't like. Salvias and zinnias come to mind. They are two of my favorites for beauty, ease of care, and long season of bloom. I have alot of deer but they have never bothered these.

As far as planting "over" the bulbs, you would do better to plant your annuals between the bulbs. That way you are less likely to damage the bulbs when you are digging holes for the annuals. It's very helpful to mark the position of your bulbs in the early spring so that you know where they are when you are planting for the summer.

I have 2 beds of Narcissus Cassata, and a tulip mix that I plant dragon wing begonias in every spring, and pansies every fall. The bed in summer is on a sprinkler system, and gets watered 3 times per week. The bulbs are fine, the tulips have come back, and the Cassata is starting to bloom already. It is a raised bed, and I top it with soil conditioner every fall and sprin before I plant the annuals.

I use the granular form of Repell All, which seems to help keep the critters away. I've read that others use Liquid Fence. Best of luck with no deer damage this year.