I just spent a few days rewriting all of my carefully ripped FLAC files to a naming structure that is consistent and easily searchable for me; however, it kept all of the ID tags that it downloaded from the server. I should have realized that tags were separate before doing this, but now would like to change them all to match. No matter how hard I search the forum I don't see this addressed. Is there an easy way to do this? Of course, to me the tags only matter when I convert the files to mp3 for play in the car. Currently when I try to change from FLAC to mp3 it renames everything to how it was and not how I fixed it.

MP3tag will do the job. It allows tagging the files based on file names and vice versa, enabling you to transfer the naming structure you created directly to the FLACs' Vorbis Comments.

Simply right-click your FLAC collection and choose "file name --> tag" (should be something like that, can't have a look at it since I'm running a few system updates on Linux right now), in the follow-up window you'll be able to configure the way MP3tag should process the data. Test your settings with a single file then, if everything worked out as intended you could make MP3tag rewrite the whole audio collection.