To open an existing workbook, change the Workbooks->Add method to Workbooks->Open and specify the filename there. Then when you close the workbook, set SaveChanges to true and leave the filename unconnected. This should overwrite the previous file with the changes without asking.
The simplest way to append the file is to keep track of the size of the table and add the number of rows to a starting point. Pass that value to the writetoexcel.vi and add it to the row index inside the loop.
If that is not possible, after the sheet is referenced, use the properties Worksheet->UsedRange->Rows->Count. Add 1 for the address of the first blank row.