I installed a premium theme prior to joining wpmu. I was having issues with getting my logo above th

I installed a premium theme prior to joining wpmu. I was having issues with getting my logo above the header divider. I contacted the developer of the them and he had me change the header height. I now have it above the header divider but its not aligned with my top menu. I'm not sure if its an issue with the image file that I'm using for my logo. Is there anyway to align them?