Hey Simon,
You can adjust the position in the css.
Find the file
plugins/system/plg_jbLibrary.php
and locate the following code
if($scrollStyle == "dark")
{
$document->addStyleDeclaration("#toTop {width:100px;z-index: 10;border: 1px solid #333; background:#121212; text-align:center; padding:5px; position:fixed; bottom:0px; right:0px; cursor:pointer; display:none; color:#fff;text-transform: lowercase; font-size: 0.9em;}");
}
if($scrollStyle == "light")
{
$document->addStyleDeclaration("#toTop {width:100px;z-index: 10;border: 1px solid #eee; background:#f7f7f7; text-align:center; padding:5px; position:fixed; bottom:0px; right:0px; cursor:pointer; display:none; color:#333;text-transform: lowercase; font-size: 0.9em;}");
}
}
Now in there you have for the dark and the light style,
position:fixed; bottom:0px; right:0px;
If you alter the bottom and right values, you can change the position of the button.
Cheers,
Jason.