Hebrews knows that the manna was kept inside the ark (there are rabbinical sources that agree). It also says (in the KJV) that the "shewbread" was in the second room, the Hekal, which seems to imply that the two kinds of bread were different... or else there is a contradiction.
In fact the apparent contradiction may only exist in the English translation. The Greek of verse 2 doesn't say "the shewbread," but has he prothesis ton arton, which means "the putting forward of the loaves." Hebrews 9:2, in other words, knows the Hekal as the room where the bread was put out (to be eaten?), but 9:4 may tell us that the same bread was kept with the throne.