I second songbird as being the current #1 media plaer/manager. For some ipoddy things it's just not as good as itunes though (audiobooks and podcasts being the main offenders, which it can't put into the right sections on the ipod)
If you want to use your ipod as a drive, for it to appear in My Computer, you have to select the "enable disk access" and probably "manage this thing manually" (I may be paraphrasing, no itunes here) options from the screen you get when you select "jo bloggs' ipod" from the source list on the left.
As to the problem with not finding files, if the songs you had in itunes have missing information (Album name, genre or artist name) they often copy to the ipod fine, but never appear in the menus, even if you select "all songs". Make sure they have something in all those fields, even if you set Album to "apple suck".
If you have a 120Gb ipod and 121Gb of media, btw, itunes will not have a clue what to do, will copy randomly what it can and then throw errors.Every time you plug in the ipod. This is clearly ideal. It's much more of a problem if you have a nano, of course. This is why I always manage music manually. A way around it is to manually make a playlist with what you want to sync, then just update that.
They don't give you a manual with the product deliberately. It's to make you realise how little you need a manual for Apple products, to reinforce how obvious everything is.