Maybe you can generate some ideas from my experience. We had this exact atrium (maybe 7 x10) in our home surrounded by master bedroom, living room, & front entryway. At one point it had the jacuzzi & plants, etc & I had made custom warm windows to insulate the windows, however we didn't really use the jacuzzi. We improved 3 rooms and built an office/attic all from this tiny area. [I will describe each thing we did by number to try and simplify]

1) So the first thing was convert the bedroom set of windows into a wall giving us more options in that room. I hated to see my custom drapes go, but the wall is much more functional.

2) Next we had the open roof area converted into a large skylight (while coincidentally re-roofing the entire house due to hail damage).

3) I had always wished for more storage space or a functional attic, so we had one of those pull down stairs installed in the center with the corresponding roof/floor structure. There is just enough space to stand in front of wire shelving to get what you need and go back down the stairs, but it's got plenty of light to find what you are looking for, thanks to the hail damage, oops, I mean skylight!

4). We took approx 8- 24" of the floor space that was on the living room side and dedicated it to running all the wires/cabling/electrical that the living room and a small office could ever need. In the living room this is now an 8" recessed area that holds the flat screen TV and a 24" recessed area with glass shelving that holds all the other components (cable box, blue-ray, etc).

5) The front entryway side was changed into a wall with built in adjustable shelving that now serves as bookcases.

6)The last side was turned into an archway type doorway (no door), to enter the new area.

7)The remaining area serves as a functional office, and allows access to cabling. The portion of the wall that consumed 8" for the TV allowed for 10" deep bookcases (with a 6"x6" cubbyhole to pass cables). The portion of the wall which encloses components in the living room has an access door in the office, painted black on one side & virtually invisible from the living room. In the new office a single long countertop serves as a desk and has space for filing cabinets and leaves just enough floor space for a comfy office chair.

The space is small, I cannot have the attic stairs pulled down at same time the chair is pulled out, or the access door open at the same time the file cabinets are pulled out. I don't need to though, I mean I can multitask but I can't be getting in the attic and using the chair at the same time anyway, & it's rare that we need to open the door to access components, so it works.

Hopefully this will give you some ideas, it took a long for this design to come to fruition. It was not a grand master plan, we actually did do it one step at a time, and lived with it for a while to help decide what to do next. I am very happy with the result, both form and function. If you had never seen the atrium, it would never occur to you that there had been one. It updated our home it terms of looking like it was made to house today's flat screen TV', DVD's, games and accessories. Have fun with your design and good luck.