Those two screws you are referring to don't actually come out of the floor, only underneath the plastic ring that is mounted to your floor. The screws only slide & lock into a groove in this ring. If, like I did, you have problems getting the nuts loose from them without turning them too, remember that there is a certain position the screws need to be in before you can properly loosen the nuts. Your new toilet will fit fine over this. Be sure to replace the wax seal - you will see this when you lift up your toilet. Also do not overtighten screws on your new commode - I read this over and over and still had to learn the hard way. Feel free to e-mail me if you need further - I just got through doing this....Saffron