I have an excel workbook opened via double-clicking it in windows explorer but cannot access it in code
Excel.Application xlApp = (Application)Marshal.GetAct
If all your workbooks are opened in the same Excel instance (you can check this by checking if you can switch from one to the other using Alt-tab). You can simply refer to the other using Workbooks("[FileName]"). So, for example :
Dim wb as Workbook //for C#, type Excel.Workbook wb = null;
Set wb = Workbooks("MyDuperWorkbook.xlsx") //for C#, type wb = Excel.Workbooks["MyDuperWorkbook.xlsx"];
wb.Sheets(1).Cells(1,1).Value = "Wahou!"