If i understand you well...
MS Excel is a single-instance application, which means that Excel will open next file in the same instance. To force creating another instance, using Interop, you need to open it using
new
keyword.
Excel.Application oExcFirstInstance = new Excel.Application();
Excel.Application oExcSecondInstance = new Excel.Application();
oExcFirstInstance.Workbooks.Open(...);
oExcFirstInstance.Workbooks.Open(...);
oExcFirstInstance.Workbooks.Open(...);
oExcSecondInstance.Workbooks.Open(...);
oExcSecondInstance.Workbooks.Open(...);
oExcSecondInstance.Workbooks.Open(...);