If you are using our default template, there are two ways to change the logo.  There are :

Overwrite Logo Images: 

By default all logo and images are located at / /application/layouts/scripts//images/ therefore you can upload & overwrite logo image to application/layouts/scripts//images/logo.png

Update the Header Block:

By default all design blocks are located at / /application/layouts/scripts//blocks/   therefore you can edit top-menu.phtml page to add custom logo location and save it.