Ideally, a document will be in correct reading order when viewed with the Reading Order Tool, and when viewed in the Tags Panel, which shows the Document Structure. This helps ensure readability with a Screen Reader, and if the PDF is saved as readable text, that text should convey content in correct order.
Unfortunately, documents do not always automatically tag in the correct reading order. Following best practices in your application can avoid but not eliminate this problem. Best practices are not always strictly possible. In MS Word best practices would demand placing all graphics inline with text. Whether you can do this depends on the document design. Similarly, text boxes that float outside the text stream may not be tagged in the order you want. The same thing happens in Indesign if unanchored Figures or Frames are used. You can create a structured Indesign document to help nail down the reading/tagging order, but it's time consuming and there's a learning curve. And still, manual tweaking in Acrobat may be required.
In Acrobat, there are a number of ways to view and/or correct the reading order. See http://www.w3.org/TR/WCAG-TECHS/pdf.html
In my opinion, making sure the Tags are in the proper reading order (Example 5 in the link above) by viewing/rearranging them in the Tags Panel and ensuring that you have set the Tab Order to Document Structure (Example 7) for all pages is the most expedient and safest choice. If you have the time, by all means correct the reading order in the Order panel, but be aware of it's pitfalls:
"Note: Reordering content with the Order panel is...for simple text content within a PDF since modifications made with the order panel can affect not only the reading order but the underlying structure of content contained within the PDF. This may impact the z-order for content on a page, including making some content become hidden behind other content. Authors should save their work before using the order panel and verify that the changes do not have adverse effects on the document."
As a final check, always checking your work with a Screen Reader to ensure things are reading properly.