This is an area that plagues most churches because little attention is given to it while the building is being built.
Not all, but many of the architects that I have worked with over the years do not really understand acoustics in relation to the literal structure of the room. Many only seem to care how if the building will pass code and how the design will look in their portfolio. Let me say that I have worked with some great architects that really "get it" but those seem to be in the minority. (Please finish the post and take a deep breath before you email me your strong disagreement with these statements.)
Like the sound system itself, room acoustics become a big concern when the first service comes around. Most "good" rooms are designed that way from the beginning. A room can be "fixed" to a certain extent, after the fact, with acoustic paneling, bass traps, and decorative wall treatments. Knowing how much treatment is enough for your room usually requires you to hire a qualified acoustical consultant to help you with type and placement. The room acoustics absolutely affect the ability to have good sound in a room. Remember you can't "E.Q." the room unless you physically change the room acoustics. Carpet, fabric covered chairs, and of course, people, can also dramatically change the way the room and the system will sound.
Note: A big sledgehammer can also help the acoustics of your building and although you might enjoy using it, it is not recommended as a long-term solution, so seek professional help on this one.