“Also, that there were two stones in silver bows—and these stones, fastened to a breastplate, constituted what is called the Urim and Thummim—deposited with the plates; and the possession and use of these stones were what constituted ‘seers’ in ancient or former times; and that God had prepared them for the purpose of translating the book.” (JS—H 1:34–35.)Then a few paragraphs later he relates the following account:
“Joseph Smith would put the seer stone into a hat, and put his face in the hat, drawing it closely around his face to exclude the light; and in the darkness the spiritual light would shine. A piece of something resembling parchment would appear, and on that appeared the writing. One character at a time would appear, and under it was the interpretation in English. Brother Joseph would read off the English to Oliver Cowdery, who was his principal scribe, and when it was written down and repeated to Brother Joseph to see if it was correct, then it would disappear, and another character with the interpretation would appear. Thus the Book of Mormon was translated by the gift and power of God, and not by any power of man.” (David Whitmer, An Address to All Believers in Christ, Richmond, Mo.: n.p., 1887, p. 12.)By putting this paragraph after the previous one, it makes it sound that the Urim and Thummin stones are the same ones that he put into the hat.
But I have found the following from an 1885 interview, where Zenas H. Gurley, then the editor of the RLDS Saints’ Herald, asked Whitmer if Joseph had used his "Peep stone" to do the translation in which his response was:
"... he used a stone called a "Seers stone," the "Interpreters" having been taken away from him because of transgression. The "Interpreters" were taken from Joseph after he allowed Martin Harris to carry away the 116 pages of Ms [manuscript] of the Book of Mormon as a punishment, but he was allowed to go on and translate by use of a "Seers stone" which he had, and which he placed in a hat into which he buried his face, stating to me and others that the original character appeared upon parchment and under it the translation in English."Here Whitmer rather clearly states that the Urim and Thummin stones and the seer stones were really seperate stones used at different times. (ie. the Urim and Thummin stones for the 116 lost pages and the seer stones for the rest of the translation)
In searching LDS.org I was unable to find any distinction between the seer stones that Joseph had since he was a young teenager (used for treasure hunting) and the Urim and Thummin he claimed to have been given with the Book of Mormon.
I'm curious if there are any other places where it is documented that the Urim and Thummin (as they were called later) were taken away from Joseph after he lost the 116 pages and if the LDS church believes/knows/teaches this. I have read that Joseph himself claimed that the Urim and Thummin stones were taken away but other than Whitmer's interview I have not been able to find the supporting documentation I've been looking for.
If the church does profess that the Urim and Thummin was taken away and the seer stones were used for the rest of the translation, they have rather carefully hidden that fact in the scriptures, talks, etc. so that they all sound like the same thing. They use the terms interchangeably to, perhaps, purposely mislead the members into believing a more sanitized/sanctioned version of the translation process.
UPDATE 07/17/2008: Bruce R. McConkie presented the following information on pg 818 of "Mormon Doctrine". It doesn't address the issue of whether or not the Urim and Thummim were taken after the 116 pages but it does confirm the existence of both the Urim and Thummim and Joseph Smith's separate seer stone.
Joseph Smith received the same Urim and Thummim had by the Brother of Jared for it was the one expressly provided for the translation of the Jaredite and Nephite records. (D. & C. 10:1; 17:1; Ether 3:22-28.) It was separate and distinct from the one had by Abraham and the one had by the priests in Israel. The Prophet also had a seer stone which was separate and distinct from the Urim and Thummim, and which (speaking loosely) has been called by some a Urim and Thummim. (Doctrines of Salvation, vol. 3, pp. 222-226.)
President Joseph Fielding Smith, with reference to the seer stone and the Urim and Thummim, has written: "We have been taught since the days of the Prophet that the Urim and Thummim were returned with the plates to the angel. We have no record of the Prophet having the Urim and Thummim after the organization of the Church. Statements of translations by the Urim and Thummim after that date are evidently errors. The statement has been made that the Urim and Thummim was on the altar in the Manti Temple when that building was dedicated. The Urim and Thummim so spoken of, however, was the seer stone which was in the possession of the Prophet Joseph Smith in early days. This seer stone is now in the possession of the Church." (Doctrines of Salvation, vol. 3, p. 225.)