In the merchant panel navigate to  Configuration > Design > Affiliate panel theme  > click 'Edit theme' at the current theme.  
If it claims to create a 'Copy of .... theme', then click yes.
Now you can look up the custom.css file and place there the following code.
.Logo {
	top: 0px;
	left: 0px;
	position: relative;
	float: none;
	margin:10px auto;
}
Then exit the theme editor and click the 'Set as default' button at the freshly created and edited theme.