Entering Data in a Modifying List

I'm trying to develop a unique list in Excel and I've realized I'm beyond my limited Excel experience. I call it a unique list but maybe it's more common than that. Here's what I need to accomplish:

• I have an Excel file that is overwritten weekly from data exported from a third-party software package (File A).
• I have another Excel file that links the File A cell contents and formats it in a way that is presentable and clear to understand (File B). File B also filters the long list found in File A to bite size chunks of information.
• Here's where I'm stumped. The problem is that File A is dynamic; there are rows filling in at the bottom but also in the middle. File A also doesn't have all the information needed. So, the bite size chunks found in File B need to allow users to enter data. After a while the user-entered cells don't match up with the correct row because File A has new entries in the middle of the list.
• I've tried filtered lists but the data doesn't match up. I've tried pivot tables but users can't enter in custom data in pivot tables (only in the source data)

Does that make sense? I've searched all over the internet but can't seem to find anything.
Has anyone ever had a similar problem? Thanks for the help!