Yes you can change the logos by editing the templates. Your login account needs permission to edit templates, but it probably has that (if you created the APE Mobile site). In the web app, use menu option Admin => Templates, then go to the Details for a template of interest. Export the Word file, and edit it to put in your own logo.
When editing in MS-Word: insert the logo image using Insert => Pictures
If you want to put it in a particular position (as is often the case) then we recommend doing that by putting it into the cell of a table, and if-desired making the borders of the table invisible.
After the above, you need to upload your DOCX file into the template then save and publish it. The steps for that are shown at https://support.apemobile.com/tutorials/making-templates/template-creation-basics-4-final-steps