Is there a BOSS type organizer for morrowind or can BOSS work on morrowind? I cannot get the hang of wyrn bash which I would love to but now I cant even get it to come up on a fresh install.

Yes, http://www.gamesas.com/topic/1398805-relz-mlox-a-tool-for-anolyzing-and-sorting-your-load-order/

Does Wrye Bash even work for MW.... I don't think it does.

You want http://www.gamesas.com/topic/1106095-wrye-mash-stand-alone/ - this version is the easiest to install/use.
The Mash documents are http://wryemusings.com/Wrye%20Mash.html which explain how to use the features.

Mash and Mlox is what you'll need to keep your Load Order and Save Files happy.