I was instructed by our vet to position the lights above the tank with the heat lamp opposite the hide. They didn't offer any site specific placement for the UV lights other than above the tank.
I have read some stories of the light not being far enough above the tank and causing some burns to the shell as well as eye problems from the UV light. When I asked the vet about this, her response was: "In nature, the sun is above us, just make sure there is a fair amount of distance (we use 2-3 feet) between the tort and the light/heat source and you shouldn't have a problem."
Our tort is only 3.5 mo old so my experience is very limited at this point so there is a good chance a more experienced owner will have better advice, however I thought I would pass along the information I was given on the subject.
I cut holes out of the top then use a staple gun to place some wire fencing around the openings so the lights can rest on that. See the second link in my signature, it shows how I position my lights on my current setup.