Let's have the metaphor in full view :
Nature also teaches me, by these sensations or pain, hunger, thirst and so on, that I am not merely present in my body as a sailor is present in a ship, but that I am very closely joined and, as it were, intermingled with it, so that I and the body form a unit. If this were not so, I, who am nothing but a thinking thing, would not feel pain when the body was hurt, but would perceive the damage purely by the intellect, just as a sailor perceives by sight if anything in his ship is broken. Similarly, when the body needed food or drink, I should have an explicit understanding of the fact, instead of having confused sensations of hunger and thirst. For these sensations of hunger, thirst, pain and so on are nothing but confused modes of thinking which arise from the union and, as it were, intermingling of the mind with the body.
(Sixth Meditation, p. 56) : http://metaphors.iath.virginia.edu/metaphors/9253.
For the record, the metaphor derives from Aristotle, de Anima, II.1. 413a8-9.
Just what does it commit Descartes to ? Its significance, as Bernard Williams suggests, is not metaphysical (in a way that would undermine dualism) but phenomenological.
Descartes never surrenders the distinctness of the soul and the body. All he admits is that there is an inessential but not absolutely accidental connection between them which is expressed in e.g. the experience of pain.
He replies to Regius (December 1641) :
It may be objected that it is not accidental for the human body to be joined to the soul, but its very nature; because if the body has all the dispositions required to receive a soul, which it must have in order to be strictly a human body, then short of a miracle it must be united to a soul. Morever, it may be objected that it is not the soul's being joined to the body, but only to its being separated from it after death , which is accidental to it. You should not altogether deny this, for fear of giving further offence to the theologians; but you should reply that these things can still be called accidental, because when we consider the body alone we perceive nothing in it demanding union with the soul, and nothing in the soul obliging it to be united to the body; which is why I said above that it is accidental in a sense, but not that it is absolutely accidental. (The Philosophical Writings of Descartes, III, The Correspondence, tr. J. Cottingham et al., Cambridge : CUP, 1997 : 200.)
Metaphysically body and soul remain absolutely separate : 'when we consider the body alone we perceive nothing in it demanding union with the soul, and nothing in the soul obliging it to be united to the body'. Separate substances can have accidental, contingent relations to each other without any detraction from their status as essentially metaphysically independent. This is the case with body and soul.
It is clear, however, that phenomenologically (accidentally, but not absolutely so) the soul can experience at least certain things that are occurring in the body. Injury to the body can cause pain, for example. As to how this is possible, Descartes' most considered position is that he does not know : in this respect the 'union' between body and soul is 'basic and unanalysable' (B. Williams, Descartes : The Project of Pure Enquiry, London : Routledge, 2005 : 267). As he writes to Princess Elizabeth (28 June 1643) :
It does not seem to me that the human mind is capable of forming a very distinct conception of both the distinction between the soul and the body and their union; for to do this it is necessary to conceive them as a single thing and at the same time to conceive them as two things; and this is absurd. (The Philosophical Writings of Descartes, III, The Correspondence, tr. J. Cottingham et al., Cambridge : CUP, 1997 : 227.)
We may note that when Descartes refers to 'intermingling' of body and soul' in the opening quote, he qualifies it with 'as it were, intermingling' : et quasi permixtione mentis cum corpore. (Descartes, Meditations on First Philosophy, A Latin-English Edition, ed. & tr. J. Cottingham, Cambridge : CUP, 2013 : 112.) 'Intermingling' is a physical process of which the soul is, by Cartesian definition, incapable.
Note on Occasionalism
Later thinkers in the Cartesian tradition such as Arnold Geulincx (1624-69) took the route of Occasionalism in dealing with body and soul. Body and soul are the separate substances Descartes thought they were but, they held, we do better to avoid even metaphorical talk of 'union'. Better to say that on the occasion of, say, my wanting to raise my arm, God occasions (causes) my arm to rise. This is, they thought, the true account of the relation of body and soul.
The Philosophical Writings of Descartes, III, The Correspondence, tr. J. Cottingham et al., Cambridge : CUP, 1997.
Descartes, Meditations on First Philosophy, A Latin-English Edition, ed. & tr. J. Cottingham, Cambridge : CUP, 2013.
Bernard Williams, Descartes: The Project of Pure Enquiry, ISBN 10: 041535627X / ISBN 13: 9780415356275
Published by Routledge, 2005.
Aristotle, Hugh Lawson-Tancred (translator), De Anima, ISBN 10: 0140444718 / ISBN 13: 9780140444711
Published by Penguin Books Ltd 1987-01-29, London, 1987 : 158.