I'm not an expert with IWP, so will leave that part of your question to others....
You have two basic options for using your scripts across multiple files:
Option 1: Write the script in the second file that does the changes you need. Use a Perform Script step in the first file to call the script in the second file. You can pass data to the second script in a parameter.
Option 2: In File 1, define a relationship linking a table in file 2 in your relationship graph (Manage | Database | Relationships). You can add a new Table occurence, double click it and use Add Filemaker Data Source to select a table in file 2. Now you can manipulate the data in this table from file 2 just as though it was a table defined in file 1.