Go by the dipstick. Every engine holds a slightly different amount of oil. What you see in the manuals is a close estimate. I'll hold back on the last 1/2 quart when refilling and top off as the dipstick dictates.
If you're just a little bit over (~1/8" or less), it shouldn't be a big deal. If you can, I'd drain down to the full mark, but don't jump through hoops to do it.
As for whether or not you should have changed the filter: I would have, if for no other reason that force of habit, but, with only 1000 miles on it, you should be OK. The oil gets dirtier during the break-in period, but modern engines aren't as bad about it as older engines. Once again I would go ahead and put a new filter on (at this point, you'll end up having to change the oil again), but you should be alright if you do you next oil/filter change a little early.
All that said, why risk it? Do another oil change, change the filter, and refill to the proper level.
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