As a general rule, you should take the time to align the floor plan as accurately as possible. The level of attainable accuracy of course depends on the quality of the floor plan image and the base map layer. For more accurate alignment, you should choose a satellite view when aligning your floor plans. If the satellite view does not provide enough details to accurately align the image, you can use the "Exact coordinates" alignment method. See this FAQ question for more information.
Accurate floor plan alignment will ensure the best possible experience for you. If there is a large deviation in the alignment, positioning performance will suffer.
When aligning a new floor plan on top of or next to an existing floor plan, it is most important that the floor plans are aligned correctly with respect to each other. To help achieving this, you can show the previously aligned floor plan as reference in the web tool. Pay particular attention to the co-alignment of elevators, staircases and escalators, to enable smooth floor transitions.