http://www.geocities.com/bjmarchini/speakerlayout.JPG

I have a 39" wide audio cart behind the seats. I would rather just put them on top an angle them away from each other a little that setting up seperate stands. Will this significantly affect my surround sound effect?

Yes.;)

Your schematic shows a 5.1 system, left, center, right, LFE (sub) in the front and two side (not rear) surround speakers. Take a look at the Dolby suggested layout (http://www.dolby.com/consumer/home_entertainment/roomlayout2.html). It shows the ideal surround placements. The introductory text says in part,

Of course, it's not always possible to place your speakers exactly as shown in our diagrams. The diagrams give a range of placement angles, so you have some flexibility. Sometimes you'll have no choice but to mount the surrounds directly behind you, but if you follow the guidelines as closely as you can, you'll have good sound.

However placing the side surrounds behind you and relatively close together will certainly alter what you hear compared to a more standard setup. That said why not try it your way first, and then move the speakers farther toward the sides just to see if you like it better.