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There isn't enough detail to give a concrete solution. A rough approach would be:
Assuming your Excel files are different formats then you would probably need to look to use a simple batch macro reading in each file and then loading to a database. On the Input tool you can get it to add the file details to the data coming out.
The output tool allows you to use a field in the data to adjust where it is written to:
If the Excel files are all the same format then it is easier. There is no need to use a batch macro as you can then use a wildcard in the Input tool to read them all in, and then use the same approach to send output to specified tables.