The gradebook by default is setup to only calculate assignments that you've graded to-date. Meaning, if a student is missing a submission and you don't tell your gradebook that it's a zero, the grade for that assignment will not be factored in. You can however, export your gradebook as a CSV (Excel file type) and it will show you an additional grading column that has that grade factored in. To prevent this from being an issue, you should enter all grades according to what has been laid out in the syllabus or alternatively, you can set a grading policy so that missing assignments automatically receive a zero. You may then go back and manually modify the grade if you choose to accept late submissions.
If you intend to use Canvas only for grades and not the rest of your course content, keep in mind that each column must have an associated Canvas Assignment and that ETM recommends that you put instructions and due dates at minimum on these assignments to help prevent confusion.