Mod Organizer is not misplacing the vanilla esms after you've cleaned them with Xedit, it's moving them into the Overwrite folder within the folder structure of Mod Organizer.
1. Why is it doing that?
The Skyrim Data folder is placed beyond the mod folder structure of MO, so there is no pre-defined place where MO could put the esms within its own folder structure - apart from the overwrite folder.
The goal of Mo is to NOT change your vanilla Skyrim game at all, neither its folder structure nor its data. So, it would be quite counter-productive if Mo overwrote your original files in the Skyrim Data folder.
That's why it copies the cleaned and the backup file of the original, untouched esm into "Overwrite".
2. What are you supposed to do about it?
a) Close MO.
b) Create a folder under "Mod Organizer > Mods" to place the cleaned esms there (you can name it whatever you like, "Cleaned Vanilla esms", e.g.)
c) If you created a backup of your original esm (something like "HearthFires.esm.backup.2015_05_31_11_37_42") move it from the MO overwrite folder back to the Data folder of Skyrim. Rename it to "HearthFires.esm".
c) Open MO and place the cleaned esm into the newly created folder within MO's folder structure.
d) Rinse and repeat.
That way, you retain a pristine Skyrim installation, yet use the cleaned files while playing.
Just in case you don't already know it: the Dawnguard.esm must be cleaned a second time to remove all duplicate records.
If you placed the once cleaned Dawnguard.esm into a mod folder within MO, Tes5Edit will use that file for the second round, of course, and not touch the original one back in your Skyrim Data folder.
The "Cleaned Vanilla esms"-folder (or whatever name you consider appropriate) should be the first one after the Non-MO entries within the left window that lists all the available mods in MO.
Unless you use optimized vanilla game textures; I'd place them right beneath their Non-Mo counterparts.
So, it might look like that:
Edited by thommaal, 31 May 2015 - 05:25 AM.