What is the best way to install flooring over the main drain in a basement?

Firstly check with the Water Authority/Local Authority that the drain is not a sewer shown on the map of sewers. If it is in fact a drain it should only serve one property, however. If it is no then it might be a private sewer that serves more than one property. If it only serves one property it is a drain and in this case and in the case of it being a private sewer it will need to be protected against damage from floor loads. I suggest you ask the advice of your Building Control Deapartment at your local Council as bot both protective measure and accessibility measures may be required.