Here's a quick code example that should help
'declare two workbook object variables
Dim wbFile As Workbook
Dim wbMain As Workbook
'set references to your workbooks
Set wbFile = ThisWorkbook
Set wbMain = Workbooks.Add 'a new workbook
'now you can manage the workbooks by referring to the objects
wbMain.Activate
wbMain.Worksheets(1).Cells(1, 1).Value = 500
wbFile.Activate
wbFile.Worksheets(1).Cells(4, 4).Value = 99
'when your done, you should release the references to the objects
Set wbFile = Nothing
Set wbMain = Nothing