It depends. If the school included the other education-related expenses on the 1098-T, then yes, you should remove them.
However, I would suggest double checking the amount the school reported on the 1098-T. Specifically, optional fees and books are usually not reported on a 1098-T. You can perform a manual check by looking at your son's final tuition bill for each semester and adding up the amounts listed for tuition and mandatory student fees. Compare that to the amount reported in Box 1 of the 1098-T. If the Box 1 total matches your calculated tuition and fees exactly, then the other education-related expenses weren't included on the form. This confirms that you are safe to keep the separate book entry in TurboTax.
If the amount you added up from the bills is lower than the 1098-T, they probably did include some additional expenses or maybe all of them, so do make sure that everything you have calculated is included. If some, not all, additional expenses are missing, you can add those to the other education-related expenses section.
