Once you open the other workbook, that will be the active workbook, and any code that runs after the "Open" command will run on that workbook, unless you explicitly move back to the other one.
I usually "capture" the workbooks as workbook variables in my VB code to make it easy to bounce back-and-forth between the two, i.e.
Code:
Sub MyMacro()
Dim wb As Workbook
Dim wb2 As Workbook
' Capture current workbook with VBA code
Set wb = ActiveWorkbook
' Code to open other workbook here
...
' Capture newly open workbook
Set wb2 = ActiveWorkbook
' Rest of code below
...
End Sub
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