I've been watching tutorials (gamer poets and dirty weasel) on setting up mods using mod organizer. I have my mods installed and according to the latest loot the load order is correct and the mods indicated cleaning being necessary have been cleaned using tesvedit. I've made a bashed patch (from within MO) but my bashed patch that was installed when WB installed has been marked "unmanaged bash patch".

I'm not sure how to describe my last issue. When i created a mod from the overwrite line and named it bashed patch it has been grouped with a few mods (in this case fus ro doh and 3dnpcv3)

It sounds like you did it right, since you created a mod from the files left in Overwrite. MO will use that instead of the unmanaged one. Make sure it's in the right place in your left pane when sorted by priority. It should be at or near the bottom.

Does the order on the left side matter to the load order at all? Also, do i clean the dlc cause loot is saying they need to be cleaned. And if i do clean those how do i get the unmanaged dlc off my order?

[edit] Have since removed the unmanaged bashed patch and do have the one from the overwrite folder which is with some other mods in a group (i don't understand this aspect of MO) but on the right side it is on the bottom of the load order.

The left side decides in what order the files of the mods are loaded and overwritten. If there are common files between two different mods the higher priority mod always overwrites the files of a lower priority mod.

DLC's should be cleaned as LOOT says. Note that Dawnguard needs some special steps. Look http://afkmods.iguanadons.net/index.php?/topic/4110-manual-cleaning-skyrim-master-files/.

not sure how to post a screen shot of my MO so that i can show what i'm talking about. With the bashpatch stuck in this group i can't change the order on the left side.

I'll use the guide to cleaning the dlc that was posted, but does that cause issues with the unmanaged mods there?

Is the left side window sorted by the priority? You can change the order only if it's sorted by the priority (click the priority text in the top right corner of the left window).

Cleaning the mods recommended by LOOT shouldn't cause any problems with the unmanaged mods.

I think you have MO left pane sorted by mod category or group. On the bottom part of the screen there is a field that will indicate this. Click on it and choose unsorted.