You may do some awesome things with your site logo in the ShortPoint Theme Builder (e.g. make the logo redirect the users to a specific page).
Nevertheless, changing the logo itself is a feature available through SharePoint Site Settings. Here are the steps:
STEP 1. Open the Site Settings.
Please click the cog wheel on the top of your site and choose Site Settings from the drop-down list:
STEP 2. Choose Title, Description and Logo.
Then, in the Site Settings menu, under Look and Feel, choose Title, Description and Logo:
STEP 3. Upload a Logo.
From here, you will be able to upload a logo from your computer or from SharePoint, as shown in the screenshot below:
Press OK to save your changes.