Indoor Courtyard Garden Advice

Hello all. My girlfriend and I recently bought an old industrial warehouse building that we are renovating into a loft residence. It has very little yard space, so we plan to add some greenspace inside the building. While repairing the roof we plan to add some very large skylights and place an 'indoor courtyard' under them. We are hoping to do something more than just a bunch of potted plants; we want actual areas of grass and perhaps a pond or fountain. This is all on a single floor with a very thick concrete foundation, so we weight should not be a problem.
We have questions about such things as providing proper drainage and choosing the right shade tolerant plants. What layers of materials should we use and in what thicknesses? If we can't place this close to a floor drain, how best should we deal with the water that drains through? We would love to find examples of other people doing similar projects, learn what problems they encountered and how they solved them. Any resources anyone can point us to would be appreciated.
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