The best landmark to use in finding the site is this Corinthian Temple monument (Bowles Family).
It is at the top of the hill near the circle, and the Craig/"MacIntyre" site is just behind it
and down the hill.  The National Cemetery is across the road, with sections for Union and Confederate fallen.

A few notes on this site:

The Craig family is well represented in the Little Colonel books.  But not completely.  Of this clan, as models for the characters, we can count Grandmother MacIntyre ( Annie McCown, or McGown Craig), Miss (or Aunt) Allison (Fannie Craig), Mrs. Walton (Mamie Craig) and her four children, and Aunt Elise (Louise Craig Culbertson) and her children, the Two Little Knights of Kentucky.  In addition, there were three brothers and another Craig sister that died years before the start of the Little Colonel stories: Alice. 

There's a poignant tragic-sweet story with that.  Alice Craig fell seriously ill in late in 1881.  Her sister, Mary (Mamie) was just recently engaged to be married to an army  Captain (later General) Henry Ware Lawton.  Because Alice sensed the end was near for her, she begged her sister to marry quickly so that she would be able to attend the wedding.  Mamie quickly sent a telegraph to Henry and he obtained leave and left for Louisville by special train.  This sad wedding took place on December 12, 1881 at Alice's death bed.  Alice died the next day.

Alice is buried next to her mother (Grandmother MacIntyre) and sister Fannie (Miss Allison). We're not sure who the other Alice is (born 1881), but guess this may have been Alice's daughter (?).  Also, there was another sibling to Fannie, Alice, Mary & Louise, a brother never mentioned in the Little Colonel stories, Harry.  By the time of the early books, he had already left home and was living in Louisville, working as a civil engineer.

Also, the relationships here in real life differ a bit from the fictionalized versions.  Starting with "Grandmother McIntyre" (modeled after Alice McCown Craig), who was in fact the maternal grandmother of the "Two Little Knights", and not the paternal grandmother as presented in the stories.

More from Census records:

1880
Annie Craig is listed with children Mamie, 25; Alexander 23; Fanny, 21; Alice, 19; Harry, 16; Louise, 14; and son Merton, 11.
(In the 1870 census, a 6 year old son is listed as "McCown", which was Annie Craig's maiden name. It is apparently Harry though we don't find him using "McCown" again in any other census.)
1900-1930
Merton was in Louisville working as a "US Gauger". In 1910 he was back with mother and siblings. Alexander and Harry were at home with Annie in 1900 and 1910 and were living with Fanny in 1920 and 1930. (at Edgewood)

 

Their Final Resting Places
(photos of the sites)

Summary Page