Congratulations on taking the plunge and "welcome to the club".
Placing the speakers on their side tends to mess up the imaging because it spreads the sound out from left-to-right in the crossover region (a couple of very important octaves). Frequency response and other characteristics should be unchanged. Don't put the speakers on their side or recessed into the entertainment center if there's any way to avoid it, the impact on the sound is pretty dramatic.
If you have to put the speakers on top of the entertainment center try them vertical but inverted and make sure the front of the speaker sticks out an inch or two from the shelf and surrounding cabinet. Something like that should sound pretty good.
If there's any way to keep the speakers vertical that would be much better. I assume you have already been given the "stands are better than shelves" lecture
re: how far apart to place them, the normal rule of thumb is that the separation should be about 2/3 of the distance from the listening position to a line drawn between the speakers, ie if you're sitting 9 feet away then put the speakers 6 feet apart.
If you could supply a bit of info about the entertainment center (or a picture) we could probably offer some very specific advice.
