Since this is a homework assignment, the best thing that you can do is ask your instructor for input. The person grading you has expectations, just like in the workplace your coworkers, managers, and customers have expectations. The expectations need to be defined by the person receiving the work.
That said, I can provide my take on how to structure a use case diagram for this particular situation.
The first thing that I would do is to identify the external-facing operations that your simulator system exposes. The text of your question identifies a few - load a configuration file, run the simulation, view statistics. Are there others? Can you pause simulations? Or adjust configuration in the middle of a simulation? Or export the statistics to various formats? Anything else that your system exposes to a user or outside system should be given a use case "bubble".
Next, I would define relationships between the use cases. The three relationships that appear on a use case diagram are extends, includes, and inherits. The extend relationship allows one use case to continue beyond the base use case. If Use Case B extends Use Case A, then all of the steps in Use Case A are completed prior to executing Use Case B. The includes relationship captures dependencies and allows behavior from one use case to be included in another. If Use Case B includes Use Case A, then the operation of Use Case A is available as part of Use Case B but does not state where during the execution of Use Case B it is used or if it is required or not. Finally, inheritance allows for a use case that inherits some of the operations of a different use case but changes or adds additional steps.
Third, I'd identify all of the actors on the use case. These would be human users or external systems that interact with the system under design. It may be wise to consider roles. Humans of different roles may have different access to functions.
Finally, I'd identify relationships between actors. One actor may be a superset of another actor, and this can be indicated on the diagram, making it cleaner and easier to read.
Scott Ambler has a good article on the use of use case diagrams and an article on reuse in use case diagrams. I find much of his work helpful when considering modeling and documenting software systems.
After all of that, I would have to recommend once again going to the person who will be using your use case diagram - in this case, the instructor grading you - to find out exactly what they need from you. In UML Distilled, Martin Fowler almost discourages the use of Use Case Diagrams in favor of other tabular or textual representations of use cases. Diagrams don't have as much value as other more detailed descriptions. Use case diagrams aren't things that you tend to see or use in industry, but you should be aware of their existence and how to read and create them should you be asked to do so.
I think you're missing the point of use case diagrams. They aren't to say, here's an actor, here's a use case. Your diagrams should be taking me through the story of a use case. That story should be more than just one oval. Whether you should be bundling multiple use cases together in one diagram has more to do with how complex the use cases are and if they fit on one page.
If you're just looking for a way to abstract similar use cases together because the rest of their story is identical then sure. Use whatever grouping picture you like. Just be consistent.
If you wish to show a multitude of something without giving each one a different label the stack has always been my choice. It's easy to do on the whiteboard as well.
With this you can start to ask, is the package box still needed? Could each oval simply be labeled "basic use case" and "additional use case"? If the oval is known to be a use case can you just use "basic" and "additional"?
Best Answer
You can put them anywhere - the top, the bottom, the left, the right. In most cases, if it fits neatly, I've seen them on the right. They go on the left if necessary. UML doesn't specify this level of detail, though. You should make a diagram that is readable to the intended audience.