The trick to creating cell references between WorkbookView objects is to ensure that both WorkbookViews share the same underlying IWorkbookSet object. An IWorkbookSet is sort of analogous to a running instance of Excel, where you can have any number of workbooks opened within that instance, and you can create cross-workbook references.
So if all of your WorkbookView objects share the same ActiveWorkbookSet, then creating cross-sheet or cross-workbook references should be as simple as entering an "=" sign in a cell in one WorkbookView and then clicking on a cell in the other WorkbookView. You should find the appropriate reference is automatically created. Example:
// Create a single workbook set containing two workbooks
IWorkbookSet wbs = Factory.GetWorkbookSet();
IWorkbook workbook1 = wbs.Workbooks.Add(); // Name = Book1
IWorkbook workbook2 = wbs.Workbooks.Add(); // Name = Book2
// Associate each workbook to a WorkbookView. Because workbook1
// and workbook2 share the same underlying IWorkbookSet, wbw1 and wbw2
// now also share the same ActiveWorkbookSet, allowing for cross-workbook
// cell references
wbw1.ActiveWorkbook = workbook1;
wbw2.ActiveWorkbook = workbook2;
// Have user press "=" in a cell on one WorkbookView and then
// select a cell in the other WorkbookView. This should result
// in a cross-workbook reference being created.
// Programmatically, you could just set a cell formula in wbw1
// to reference a cell in the other workbook.
wbw1.ActiveCell.Formula = "=[Book2]Sheet1!$A$1";