You can mount them on top... or on the sides. That's up to you.
Originally, I was going to mount mine on the top rails, but it was going to be in the way of my controls, so I did a side mount. The aluminum frames on these tops are very flexible, and it was easy to pull it out a few more inches. I would recommend a side mount, just to make sure everything clears. Also... if it's wide enough, you can just fold it back on the aft deck.
The solid rear stays are a very good idea. I only ran the straps for one year. As far as the length goes... you won't know until you are trying to mount them. I don't recommend buying the adjustable stays. First... they are known to slip... and second, they are expensive. What I did was to buy a set of generic fixed length stays. (Relatively long) I think they were only about $20 with all the hardware. Then... I put the mounting hardware where I needed it to go... and then re-worked the stays.
The stays are basically an aluminum tube with plastic ends pop-riveted on. I just drilled the rivet to remove the tube end. Then, I figured how long the tube needed to be. After that... I just cut them off, and drilled new holes, and put a bolt though it, to hold the end on. (Easy)
A few tips on the install......
When you drill the holes... make sure you come back with a big drill bit and cut the gel-coat. (almost like a countersink) The reason for that is... when you thread the screws into the hull... the fiberglass is strong, and slightly flexible. BUT... the gel is hard. So... when you start threading the screws in... the gel will chip and crack. If you cut it a little bigger than the screw hole... you will keep it from cracking, and the mounting hardware will cover it.
Also... get yourself some "Thumbscrews" for the mounting points. That will make removing the top for storage very easy.
Here's a few more mounting pics, with the solid rear stays.