The easiest way is to be proactive. As you note, you can really only grab the name of the active workbook. So grab and store the first workbook name, then when you open the second workbook, it becomes the active book, and you can grab and store that one.
If both books are opened before your code even runs, then all you can do is loop through all the open workbooks and parse out the names you want/don't want.
Code:
Dim wrkbk as Workbook
For Each wrkbk in Workbooks
wrkbk.Name = myvariable
Next wrkbk
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