Alan runs a business not only in China but also in Thailand
Or is this better?
Alan runs a business in not only China but also Thailand?
The first statement Alan runs a business not only in China but also in Thailand is the correct declaration. It justifies your sentence as there is a business not only in China but also a business in Thailand.
However the declaration Alan runs a business in not only China but also Thailand? is an illegal declaration according to English sentence construction.
It does mean the same, However the construction has to be Not only in___ but also___ , you may take it as a general syntax of construction.
Also to note that your first statement Alan runs a business not only in China but also in Thailand can be modified by eliminating the second in i.e the statement can be rewritten as
Alan runs a business not only in China but also Thailand.
I find both sentences a bit lacking. All businesses need some sort of legal license, and China can't license a business in Thailand. The first sentence is the better of the two and sounds ok, but when you parse the sentence you could interpret it two ways. So does Alan have (1) multiple sporting goods stores with some in China in Thailand or (2) A sporting goods store in China and a drug store in Thailand?
I like these better:
The sentences above make the point more clearly if Alan has one business or multiple businesses.
As Cambridge Dictionary shows the structure is always "not only A but also B where A and B can be a word or a word group. http://dictionary.cambridge.org/de/grammatik/britisch-grammatik/not-only-but-also
You don't find "A not only but also B. I would consider this an unnatural word order.