There are various sources that can be used to get some idea of how to go about Nautical Archaeology.
Also be aware that there are various organisation that will need to be involved with your project.
If you plan to put a buoy on the site for more than 28 days or want to investigate the site by digging you will need to contact the Marine Management Organisation (MMO) for a licence
If you recover any artefacts you need to contact the Receiver of Wrecks They will decide what happens to these artefacts
If you find anything of historic importance you will also need to contact English Heritage who will advice you how to proceed and if necessary give the wreck protected status.
If your project falls into a Marine Conservation Zone (MCZ) then this may affect what you can do on the site