The quantity takeoff report is displayed in a default XML format and needs to be styled using an FDOT style sheet.
Navigate to the folder with all the FDOT style sheets and select the appropriate tabulation style sheet. Tabulation Spread sheets are found in the FDOT2012.C3D\Data\QTO Reports\Style Sheets. This is where you will select the stylesheet that corresponds to the Pay Items that you selected previously.
The tabulation style sheet will create a different XML file which will need to be saved into the project folder structure.