How inputs are run through tools - individually as distinct runs or combined/used together - depends on the way the tool form is designed. Some only do one, some the other, and some will do both. The tool form describes how the inputs will be used, as would a small test, but we can help if that is confusing. Also, once you use a few, it will become clearer.
In short: if the option to "multi-select" inputs is used and multiple datasets are selected (including collections), the inputs will run through the tool individually. Others tool forms allow additional datasets to be added in distinct sections - this is when the inputs will be run through the tool together.
If you are not sure about a particular tool, just ask. Specify the tool by name and version, where you are running it (by URL, or local, etc), how the inputs are entered now (screenshot helps here), and how you want the data to be processed (individual or combined).
Thanks, Jen, Galaxy team