Default Magento theme allows you to set the position of product options from administration. To do that, choose a product that you want to edit and from the left side menu open ‘Design’ tab. Second option from the bottom should be ‘Display Product Options’ in a drop-down selection, with options ‘Product Info Column’ and ‘Block after Info Column’. First option will set the product options to be displayed next to the products main image (case with most standard/popular themes), while second option will put the product options on the bottom of the page as a separate block.
First layout is excellent when products have a smaller number of product options and are related to products image, for example Color Swatch, which updates the products image when attribute option is selected.
Second layout is more convenient when products have a larger number of options and require a bit more space. In this case, it is good to have the price on the top and the bottom of the page (price clone) so customers can see the price update when they select the attribute option, otherwise they will need to scroll to the top of page.