You definitely don't want them on top of the tray, because you want the center of gravity close to the axles. I mounted mine on the bottom of the plate when I built it, but it was temporary. I'm in the process of moving the elecronics down closer to the axle now.
That's the beauty of a crawler, there's no set way to do anything, you can move stuff around to best suit your needs. I'm in the process of moving my electronics do closer to the axles to get ready for the comp. I'm mounting my receiver and ESC on the upper links. You can buy link plates, but the ones that I've found are made of aluminum. I didn't want the extra weight above the axles, so I made mine out of lexan. They are mounted on the upper links with zip ties, so they will stil flex and will not interfere with the suspension one bit. I'm attaching mine with velcro, so I can remove them and reaatach them with no problems. I'll include some links to the plates so you can see the basis for the design that I'm making out of Lexan. I'm going to order some carbon fiber to cut them out, but the lexan will do for now, and that's what a lot of the big comp guys are using. I look at the setups that some of the big dogs use, and at least I know it's capable of working out good.
http://www.ckrccrawlers.com/shop/index.php?main_page=product_info&cPath=24_56&products_id=1033
Axial realized that this was a better design than under the battery tray, and just released these.
http://www.axialracing.com/ftp/ax10options/ax30497_upper_plate.html
Another option is to cut the battery tray in half, and move the lateral braces that hold the battery tray into the holes further down on the chassis. You basically cut the stock battery tray into three pieces, and get rid of the middle. That way, you still have the stock mounting holes and brackets so it's an easy conversion. It lowers the COG, but not quite as low as mounting on the upper links.
http://www.rccrawler.com/forum/showthread.php?t=84882&highlight=electronics+tray
You guys really owe me, I just spent an hour looking for that thread because I'm at work and my favortites are on my home computer.
I also replaced my aluminum battery tray with graphite to cut down on the weight. I thought about using the battery plate method above, but with the graphite it lowers the weight a lot, and still give chassis strength. Also, I'm switching over to a blackjack comp chassis and the link plates work a lot better on that setup.