For skins that use a site logo you should be able to choose the logo from Site Settings and it will show a list of image files from /Data/Sites/[SiteID]logos
So you can just add your custom logo to that folder.
If you don't see the dropdown for site logo in Site Settings it means it is hidden by CSS so you need to unhide it. Search for ".logolist" in your CSS as indicated in the article Where is the Site Logo
Hope that helps,
Joe