Here's what I did in my Life States Dynasty:
Built a room that was 9x6. The Regifted Window is 3 wide, so I could stick 2 on the shorter sides, and 3 on the longer sides. On the one side where I wanted the door, I used Window Schmindow to fill in the gaps (it's the single tile version of Regifted, and both are full length with no breaks).
Built a 2nd floor, and repeated with the Regifted Windows all the way around. Do not put a floor down. For the roof, use the Flat Roof. Don't forget to do wall coverings!
In buy mode, under roof decorations, you'll find the ceiling pieces. Arrange them however you like, when they're on the flat roof, the roof becomes invisible.
For the plants themselves, you can approach it three ways:
1) Put all non-tree plants in the planters, stick them inside. Lay down desired flooring. Put trees outside.
2) Put all non-tree plants in the planters, stick them inside. Lay down desired flooring, except in the spot you want the trees. Put trees inside (I usually just use MoveObjects On for this). Trees growing indoors would break the floor of the 2nd story. Using this method, I strangely didn't have the unfinished room moodlet.
3) Plant everything on the ground, don't put down any flooring. This will give you the unfinished room moodlet, but it's hardly a big deal. Again, MoveObjects On is a big help here.
Since you have the greenhouse, I assume you also have the SwiftGro gardening station? It will water everything inside the area at 7am and 7pm, regardless of planter use - contrast with the sprinklers that do not water anything in planters.
That's what I've done so far, anyway!
