1.  U.S. Census, 1810:  Christian Co., KY (extracted from Microfilm Roll 252-9 by A. Robert Matthiesen at the Santa Clara County Genealogical Society, San Jose, CA).  See 1810 Table. 
There are four John THOMPSON households in the 1810 Census of Christian Co., KY.

Two of these John THOMPSON households have nine children, each with four boys and five girls.  What primarily differentiates these households is the ages of the couples:  one couple is over age 45, the other couple is age 26-45.  (The childrens' ages would be useful, too, if we knew them all.)  Also of significance, the younger couple is living in the part of the Christian Co. that later became Todd Co.  Based on evidence other than the census, we have two John THOMPSONs who should be in Christian Co. in 1810, each of whom was known to have four sons and five daughters.   One of the couples is Capt. John THOMPSON (b. 1752) and his wife, Mary JEFFERS (b. 1756/7).   The other couple is John THOMPSON and Sophia BEST (ages unknown).  This John died in 1816, and his widow shows up in the 1820 and 1830 censuses of Todd Co.   Clearly, Capt. THOMPSON and his wife have to be the older couple in "Christian" Co. while John and Sophia (BEST) THOMPSON must be the younger couple in "Todd" Co. 

The other two John THOMPSON household must be the husbands of Amy BOBBITT and Elizabeth SPENCER.  John THOMPSON and Amy BOBBITT were married in Christian Co. in  <oops -- big thunderstorm, must stop> 

2.  1820 KY Census Index (online at GenealogyLibrary.com):  Christian/Todd/Trigg Cos., KY.  See 1820 Table. 
There are two John Thompsons and one John R. Thompson, all in Christian Co.  One of the John Thompsons must be the husband of Elizabeth SPENCER, though I don't know yet which one he is.  The others remain unidentified.

3.  1830 KY Census Index (online at GenealogyLibrary.com):  Christian/Todd/Trigg Cos., KY.  See 1830 Table. 
There are five John THOMPSONs, three in Christian Co. and two in Todd Co.  Two of the ones in Christian Co. must be the husbands of Elizabeth SPENCER and Amy BOBBITT, though I don't know yet which each one is.   One of the three John THOMPSONs in Christian Co. is almost certainly the father of Martha E. THOMPSON, who married Gabriel LONG.  The others remain unidentified.

4.  1840 KY Census Index (online at GenealogyLibrary.com):  Christian/Todd/Trigg Cos., KY.  See 1840 Table. 
There is only one John THOMPSON, in Christian Co., and he has to be the husband of Elizabeth SPENCER.^A  There is an Amy THOMPSON in the 1840 Census of Christian Co., who is most likely the widow of John THOMPSON.^B

5.  1850 KY Census Index/Microfilm (online at GenealogyLibrary.com):  Christian/Todd/Trigg Cos., KY.  See 1850 Table. 
In Christian Co., there is one John THOMPSON who has been identified as the husband of Elizabeth SPENCER, and one John G. THOMPSON who is an unidentified 18-yr-old boy not living with his parents (and not head of household).  There are no John THOMPSONs in Todd or Trigg Cos.

A.  John THOMPSON and Elizabeth SPENCER were married in Christian Co., KY, in 1806; and they show up together in the Census of Christian Co., KY, in 1850.  It is reasonable to deduce that John and Elizabeth (SPENCER) THOMPSON lived continuously in Christian Co. between 1806 and 1850 and that he therefore is one of the John THOMPSONs in the 1810, 1820, and 1830 censuses and is the only John THOMPSON in the 1840 census.

B.  John THOMPSON and Amy BOBBITT were married in Christian Co., KY, in 1806; and Amy shows up in the 1840 Census of Christian Co., presumably as John's widow.  It is reasonable to deduce that John and Amy (BOBBITT) THOMPSON lived continuously in Christian Co. between 1806 and 1830 and that John died some time before 1840.