Depending on the NWN@ structure being used, I do one of the following.
A - Paint a door into an existing house or other small building set using the tileset options, then overlay the placeable building overtop of the tileset structure. This can be abit tedious and difficult to manage, but eventually it'll become second nature and only add a minute to an area's building time.
B - Add a building/doorway using tileset options and put in your door. Then, using the left hand collumn of your toolset, find the door you painted. Right click it there in the doors list for your map and choose the "Adjust Location" option. Move it by adding/subtracting to the X or Y axis' until it's on a different tile square. Then you can erase the tile you used for a doorway and your door will remain "floaty" wherever you moved it too. Place your NWN2 Building and then adjust the doors location as before until it's where you need it. This option is easiest for most as once the door is close, you can nudge the placeable to match up to it. Doors can only be moved from the lefthand collumn of the toolset under the area they are in, clicking the doors themselves does not offer this option like it does for placeables.
Hope this helps.