Angier moves the bodies to the old abandoned Theatre that he rehearsed the show in, to clear them out of the Theatre he was performing in, and does this nightly after the show. The blind stage-hands will assist with this process, as they have no idea that they are transporting bodies in the tanks.
There is no indication from the movie that he had any particular plans to dispose of the bodies properly once the run of performances was over, but also no indication to the contrary. Perhaps he intended to deal with this personally once everything was over - he could rely on no-one else to do this for him, and it is a final affirmation that he 'got his hands dirty' to be a great magician. Perhaps he even planned all along to burn the old theatre down, though clearly not in the circumstances that occur at the end of the movie.
As someone who meticulously planned this final act, to crown his achievement as the greater magician, and frame Borden for his murder, it does seem strange that he did not dispose of the body each day - as it was clearly a risky plan to store the bodies for some period - but it is not inconceivable that he planned to get rid of them eventually.