Now that you understand how to import a DTD into F+S, it is time to be sure of your Schemas. Make sure that F+S understands 100% of your DTD, i.e. that there is a good match between EDD and DTD (IMHO this is not a problem for beginners, problems start when you want to use advanced Schema features of F+S).
Probably you want to make changes to your DTD. There is even a chance that you will have to redesign your DTD. You can't use attributes as you are used to have in your XML world. Also some elements better become attributes if they are not meant for printing, e.g. before you filtered these out with XSLT (else you have to learn additional F+S techniques). You don't want to generate PDF from XML but rather do it directly from FrameMaker
Unless you did something completely wrong so far in which case you might want to restart with a new EDD, you can import (instead of opening) your DTD. F+S will automatically adapt the EDD to the new DTD structure. I made several important modifications and everything went well. You modify your EDD anytime you want (even while you are authoring), however you may loose formatting information and may need to adapt your text to a new DTD/EDD.
Menu: File->Developer Tools->Import DTD (with the EDD file active!)