I think the preferred location for the stereo is in the t-top's electronics box. You may need some type of gimbal mount enclosure, if the stereo is the standard din, (auto) type. It basically becomes like a VHF.
You can also mount "box" type speakers on the outside of the electronics box, (if there's room). This is the easiest because all of the wiring, (including the antenna) is right there.
You could install the flush mount type of speakers in the electronics box as well, but I wouldn't. If you go with that type, I would do what Gross Profit did.
Here's an example of a gimbal mount;
http://www.boatersworld.com/product/319 ... Bciav-accs
Another mount. This accepts either din, or the old shaft type;
http://www.boatersworld.com/product/319 ... Bciav-accs
There are some stereo's that include the housing, Jensen, JBL, etc. I can't find the JBL model, (Boaters World) on line, but they may have them at the store.
Here's a Jensen. Doesn't show the enclosure, but it's mentioned it the description;
http://www.boatersworld.com/product/316 ... io-systems