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.