Congratulations. As an owner of the exact same combination, I'm sure you'll enjoy the camera and lens. Tip: If you don't have one already, get yourself a flash gun. I've had one since April, and it's the best accessory I could have ever bought. Read my review here
You can use the filter together with the hood and lens cap. The hood fits round the lens, and the filter is no larger than the lens, so the hood fits around that too. The lens cap can be attached on the front of the filter.
I'd recommend using the hood at all times, so leave it on every time you put the camera in your bag. Unless you're using the pup-up flash at wider focal lengths (eg. 16mm), it won't appear in your image (at 16mm with flash, you'll see a shadow).
Best is to use all of them, hood, cap and filter. Leave the hood and filter on at all times, and only use the lens cap when the camera is in your bag or if you're not using it for a longer time.
Of course, the filter is there to protect the front element of the Zeiss lens, but it's wise to use the lens cap, because that's cheaper to replace than the filter.
- Bjorn -