Without seeing what you are trying to do all I can say is...
Build a two dimensional array with your X and Y values.
Use the Array to spreadsheet function to save the array to an xls file
you will end up with two columns containing your X and Y values
If you are using the write to spreadsheet file function then you are not actually writing to an Excel file. What you are writing to is a Tab delimited or Comma Seperated file that Excel can read. In order to write to a "True Excel File" then you have to use the Report Generation Toolkit or you must manually do it through Active X components.
Please post what you have done and we will be able to assist you furthur. It is really just a matter of building your array correctly before you write it to the file.
Instead of open/array to spreadsheet string-write to text file/close, you can pass array to Write to Spreadsheet File VI (see attached image) with the required delimiter type.