Find pandorajar.css, it's located in skinsdefaultcss in you Pandora directory. Edit with notepad and find the following section:
#TunerContainer iframe {
width:684px;
height:360px;
margin-left:-44px;
margin-top:-110px;
border:0 solid;
}
Margin-left and margin-top offset for the ads. Adjust these values to get the player to position correctly. Save the file and then reload Pandora's Jar.