The differences between the FLDS and the LDS are that the FLDS still practices Polygamy as it was laid down in Mormon scripture D&C section 13, and the FLDS follow a different living prophet (although they do still recognize the same founding prophets)
LDS believe in polygamy, but do not practice it on earth at this time since it is against the law.
Here is a link to the proclamation discontinuing the living practice of polygamy within the LDS Church. the Wilford Woodruff Manifesto (from LDS.org)