Usual method would be employing a floating dry-dock, as was done for the German Fleet at Scapa Flow or the Kursk in recent years.
Also in passing...
Not quite for the Kursk. She ended up in a Floating Dock but that was very much the last phase. The primary recovery asset was the barge
Giant 4, fitted with Strand Jacks and a system to compensate for heave casued by wave motion. Kusk was lifted into contact with a frame on the bottom of
Giant 4, which was then fitted with pontoons to lift it clear of the water to allow it to be floated into the dock, lower and then realease the
Kursk and withdraw.
There used to be a very good site around that followed the recovery in near real time and then formed a record but this is the best I can find at the moment (a .pdf)
http://www.largeassociates.com/kurskpaper.pdf Rick