Generally speaking, only one file should be uploaded to any version - that is, the one that most people will want to download. There are certain cases where additional files are permitted:
Source files: For Java-based projects (mods and plugins), uploading a JAR file containing source code created by a build tool such as Gradle or Maven is acceptable.
Javadoc files: For Java-based projects (mods and plugins), uploading a JAR file containing a generated Javadoc is acceptable.
Resource packs associated with a data pack: For data packs, it is acceptable to upload a resource pack as an additional file. Make sure to select the "Required resource pack" or "Optional resource pack" file type as appropriate.
Configuration templates: Any default configuration file(s) that cannot be included in the base file can be uploaded as an additional file.
Outside of these cases, the "Additional files" section should rarely, if ever, be used. Separate files supporting additional loaders or game versions must be uploaded as separate versions on a single project. It may be appropriate to create an entirely separate project for different variations of a project.