The store fields such as Store Name, Logo, Email Address, Phone Number, etc. are determined based on the store settings.
To edit these fields, follow the steps below:
Click Settings (the Wrench icon in the upper right).
Next, select Selling Channels and then Store Setup from the sidebar on the left. 
Click Edit under the actions section and then you can edit the store information which will populate on your emails.
Follow these steps for each active Selling Channel.
Please note that the Store Logo Size will vary based on the original image uploaded. If the logo size isn't suitable, adjust the dimensions using image editing software, and reupload logo. The recommended logo size is approximately 300px by 80px.