To select the shapefiles at runtime, you should design your workspace to have a File/Folder parameter. See this article - https://support.safe.com/hc/en-us/articles/26633456986637-Published-Parameters-in-FME-Form
For dynamic writing with geodatabases, there are multiple ways; you can use attributes as names (no run time interaction with this) or use parameters for your destination filegeodatabase or its feature types (AKA feature classes), as well. This is an article that will show you how to use date attributes as names of output files or features - https://support.safe.com/hc/en-us/articles/25407603257997-Including-Dates-into-the-Names-of-Output-F....
Type of format matters, whether its file based or folder baed like geodatabases.
Note that when using the term Dynamic Workflows in the Workbench app, it is a more advanced technique thannnnn what you are asking and it usually involves schema setting/mapping. It doesn't sound like that it is your question.
Ask if you have additional questions. BTW, I'm moving this question to the Data Interoperabiliy place Since your question is more specific to the features of the product. Thanks!
