Anonymous4401, from an earlier post on this page:
And, the other thing I'd like to point out, is during this time, most Kentuckians wished to remain neutral and not take part in the conflict. When Major General Polk ordered troops into Columbus, Kentucky on September 3rd, 1861, Kentucky no longer was "neutral" and that is when they had to take sides. Brigadier General Grant took Paducah on September 5th, 1861.
By November, 1861, the Union had control over Louisville, Paducah, Frankfort, Lexington, and other cities in northern Kentucky.
The Confederacy had control over Columbus, Bowling Green, London, Pikeville, and other cities in southern Kentucky.
This is the way it is currently set up, based on November, 1861. This was because I didn't have accurate sources or figures for the period June/July 1861 (or August through October for that matter, except the Paducah and Columbus occupations). Now, I have reasonably accurate figures for troop deployments in June/July 1861. Some areas I'm going to have to improvise on though and guestimate. (guess and estimate)
So, to answer your question, yes the Union and Confederacy did eventually occupy Kentucky (September-November 1861), but in June and July of 1861, it was "neutral" in the eyes of both Union and Confederacy, as well as in the eyes of most of its leaders (including the Confederate-leaning governor).
I hope this helps.
Edit: Brigadier General Pillow's troops were the ones who actually occupied Columbus on Sept. 3rd, Polk though was his commanding officer and immediate superior. Polk later gained permission from President Davis for the move, but at the time it had been opposed by the Secretary of War of the Confederacy, as well as A. S. Johnson (opposition to it was after the fact).
Edit #2: If anyone can supply some troop deployment figures for the Union armies in Illinois, Indiana, Ohio, and Missouri for the period June-July, 1861 (or even May would be useful), and the Confederate armies in Tennessee and Missouri for the same time period, this would be most helpful.