You may place a siddur or chumash flat on chair seat or bench on which no one is sitting, but it is an act of piety to stand it up on its edge. 
To sit on a bench or other seat where a holy book rests, raise the book up at least a little; a single piece of paper is sufficient elevation.
NOTE If you are sitting on a bench and someone puts a holy book on the bench, you must stand up or raise the book off the bench. You may not stand a siddur, chumash, or other holy book up on its edge on a bench or pew in order to be allowed to sit on that bench.