Hi @IsaacHclark,
I'm not really familiar with Matlab grader, but I can pretty confidently say that unless Matlab grader can handle the short answer questions itself, you won't be able to accomplish what you're looking for in a single assignment. You can select the type of assignment (or quiz) in Canvas, but you can't mix and match external tools and internal Canvas functionality together in a single assignment. You'd probably want to make one assignment with the external tool submission type for the Matlab auto-graded content then another assignment or quiz for the short answer questions. This is a bit more work on your end, but if you title the two things similarly ("Week 1 Assignment Part A" and 'Week 1 Assignment Part B", for example) I think your students will probably catch on very quickly.
Hope this info helps!
-Chris