I have been following this guide http://www.reddit.com/r/skyrimmods/comments/272pwi/super_epic_guide_beginners_guide_section_23/

I followed pretty much everything here, except for the enb section.

I watched the video tutorial how to run Tes5edit. and did that exactly as was stated.

I have selected skyrim and update, applied a filter only to update, cleaned identical to master records then undelete as he did on the tutorial. and saved .

I repeated this with updated - skyrim - dawnguard (only applying the filter to dawnguard) and then the same procedure with hearthfire.

but now mod organiser has given me a warning "there are files in your overwrite mod"

As I have not encountered anything about this in from the reddit tutorial, I decided not to take the suggested action of mod organiser, which is to reorganised the overwrite mod, but instead check with people who understand what this means??

Also while I am here, exactly how many of these mods should I clean? All ??? and if so should it be in load order (ie top to bottom) and should it include the unoffical patches? I ask that because in the tutorial I noticed that gopher also had the unofficial patches, but he moved from dawnguard to hearthfire and excluded skyrim unoffical patch / dawnguard unofficial patch. Which as far as LOOT is concerned the correct load order should be skyrim-update-skyrimunofficial-dawnguard-dawnguardunofficial. So shouldn't the cleaning order follow ? IE Skyrim-skyrim unofficial-dawnguard-dawnguard unofficial?

thanks everyone

Edit : also MO shows a paper clip icon next to skyrim unofficial patch? what does that mean?