I'm trying to identify a book from either the 1980's or 1990's. Cover is a man sitting on a throne of bones. The protagonist is a Galactic secret agent, who gets decapitated and has his head reattached by his handler, a woman. On one of his missions he shoots down a plane with a missile launcher. The man visits a woman in a psych ward. She hates him, and it is revealed that he is insane. The protagonist and the woman grew up together and he may have killed the woman's brother.
That’s Use of Weapons by Iain M Banks, the third novel published in his Culture series. I’m not familiar with the cover you describe, but all the plot elements are there, and a chair made of bones is also an important element of the plot. Are these names familiar: the protagonist is called Cheradenine Zakalwe and the sister he visits is called Livueta?
Note that there’s a plot twist at the end of the book which is revealed in the Wikipedia link above, and makes it difficult to describe the plot without serious spoilers.