[Nawm]

First. I would like to remove the ".." up option I get with my TV shows, movies and music as I do not use it and would like a cleaner look to it.

Second. I have 4 different TV shows (Doctor who, Torchwood, Breaking Bad, and Archer) in a directory as " TV shows/Show/Season#/#-Episode.m4v" Now Doctor who is showing up with everything but the other 3 are not.

Third. I am not receiving any cover art for my music.

[artrafael]

First. I would like to remove the ".." up option I get with my TV shows, movies and music as I do not use it and would like a cleaner look to it.

System > Appearance > File lists > Show parent folder item (deselect)

[TRaSH]

for your first issue as posted in the post here above,
but you could have found it also by reading the wiki (wiki) and looking through the settings menu

for your second issue i would suggest to add a debug log (wiki)

for your third issue i would suggest to look at the following add-on:cdART

[HenryFord]

Archer

For Archer, choose the directory name "Archer (2009)", because there is an old series with the same name (I suppose you mean Archer from Adam Reed, first aired in 2009)