A proper ZIP file will make life easier for the grader or user of your ZIP. It is easy to do. An incorrect submit causes headaches for the grader (and score markdowns).
Only submit one ZIP file with an assignment/drill unless otherwise noted. ZIP files have a ".zip" file extension. Only ZIP format will be accepted. Do not submit ".rar", ".tar", etc.
Typically a ZIP file will be the only file you submit with an assignment (of course the remainder of the your files will be within the ZIP).
Avoid duplicate names. E.g. if one file you are submitting is MyCoolObject.java but you submit multiple copies of that file (in different directories) the grader may pick up any one, and not necessarily the one you expect.
If you need to submit MyCoolObject.java, it is also yes okay to submit files like MyCoolObject.class, which will be ignored (no impact). It is generally okay to submit "extra" (ignored) files, just be careful not to submit duplicate JAVA files.