All molecules have a 3D shape, but some are symmetrical,some are essentially flat but others (especially in Organic Chemistry -the chemistry of carbon compounds) very many of them have non-symmetrical 3D structures. Chemists often draw compounds in the flat skeleton you are using when the stereochemistry (their arrangement in 3D space) is not important as when they are just trying to give a drawing of the way one atom is bonded to another in the molecule. What is the purpose of your drawing? If it is just to show the arrangement of the atoms in the molecule, which atoms are joined to which, then your drawing is probably OK to be rotated or flipped - that doesn't change with orientation. However, if you are trying to show the absolute positions of the atoms with respect to each other in space then it does matter. Chemists can draw these 3D structures even in 2D using the convention that John referred to - if some atoms are sticking "out" of the plane of the paper with respect to the main body of the molecule the bond connecting it to the flat part is shown as a solid wedge; if the atoms are sticking "behind" the plane then they are shown as a "striped" wedge. If you want to see this, go the the Wikipedia page on stereochemistry (Stereochemistry - Wikipedia ) and in the diagram at the top, look at the two structures near the word "enantiomers" - the drawing shows the chlorine atoms as sticking out of the page and the fluorine as sticking behind. You can rotate that structure on the right hand side around the plane of the C-H bond and make the bromine into the solid wedge but then the chlorine would become the dotted wedge and the fluorine would become the straight line (in the plane). It all has to be consistent to be an accurate drawing of the molecule. Some molecules have biological activity ONLY if they are a specific 3D shape so if you are illustrating this - even in 2D - it is important to use the drawing conventions to indicate the 3D shape. In that case if an image is rotated or flipped then all the 3D indicators have to be kept consistent with the original image. So it comes down to what you are illustrating - is it just the position of the bonds from one atom to the other, or is the 3 dimensional arrangement also important? BTW the Wikipedia article on skeleton structures is also pretty good at explaining some things if you are not a scientist in terms of the conventions that scientists use. Skeletal formula - Wikipedia
