Okay, I think that both of your questions can be answered with at once, so I am gonna go ahead and reply to this only...
I have the the files on my computer, I add the files to to the iTunes liberary, then i selected the music i want on my iPod, then i transfer the files, wait for gapless playback thing to be proccesed, then I check in iTunes if the music is on my iPod, which it is, then i add the differnt tracks to the "correct" playlist, i can play the files under iTunes from the iPod, then I disconnect the iPod with the eject button in iTunes... Now i look for the newly added files on my iPod, they are nowhere near to be found, neither playlist, artist, song, search or whatever, I can't find the files... Then i connect the iPod to my computer again, look under iTunes, the music is still under my computer liberary, but it is missing from my iPod liberary, both from the playlist and the music liberary... So naturaly i assume that the files has been deleted from the iPod, but under the status bar for my iPod, there is now a amount of data shown as other wich corresponds to the amount of data that i have just added... Then i go inside windows pathfinder, locate the iPod drive, go inside the ipod control/music folder, and add all content from this folder (i.e. the F0X hidden folders) to winamp, now here i can see all the music i just have added, with the correct id3 tag, well a few is just shown as the four letter random word that iTunes gives the files (i.e. missing id3 tag)... They all are able to play under winamp... So obviously the files aren't deleted...
So now I have to compare the iTunes iPod playlist and the winamp playlist, and then delete all the files in pathfinder that are shown in winamp but not in iTunes iPod liberary, as you can imaging this takes alot of times when when we are dealing with so many tracks, cause I just can't readd the files again without deleting the tracks, because then they are on the iPod twice, one version not on iPod's playlist and one version on the playlist...
So you can see my frustration for have to doing this each and everytime...