You can create a PS Query and save the definition. In PeopleTools 8.46 you can run a PS Query as a process. In otherwords, you can schedule it to run through the process scheduler.
When you run the Query through Process Scheduler you can choose the output type of Web and the Format of PDF.
You can't add a logo to a query by itself. You will either have to create a Crystal report using your query, or depending on what version of tools, you can use the XML Publisher to accomplish what you are asking.