In the merchant panel navigate to Start > Configuration > Design > [Affiliate panel theme OR Signup page theme OR Merchant 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.
.HeaderInfo {
height: 94px; /* change this value to suit your logo height */
}
.Logo {
width:314px; /* change this value to suit your logo width */
height:57px; /* change this value to suit your logo height */
top:20px; /* change this value to decrease/increase the distance of the logo from the top of the page*/
left:22px; /* change this value to decrease/increase the distance of the logo from the left side of the page*/
}Then exit the theme editor and click the 'Set as default' button at the freshly created and edited theme.