I think I understand what you are saying but I do struggle with using iTunes. I've never found it user friendly and it does confuse me. Admittedly I'm not very good at syncing frequently so when I do, I tend to forget how to use it properly! Basically, when I download a song from iTunes onto my phone I add it to a playlist I have created. I understand that it stays in my list of songs on my library but for example, once I moved the xmas songs into iTunes on the computer yesterday, I then moved them via my phone into my 'Christmas' playlist which I had created. I was disappointed to only find one song in that playlist when I had already moved an entire xmas album several months back so I now have to find time to move them all back onto that particular playlist. Likewise, the 'September 18' playlist I had created included songs that I had downloaded over the summer as well as songs I had downloaded over the last couple of years which I added to that playlist too. After I had synced my phone with the computer yesterday, the only songs that were in this playlist were the ones I had added over the summer and not the ones from previous download sessions. Does that make sense?
I guess I use my phone more to create playlists and move songs around rather than doing it on the iTunes on the computer. Am I doing this wrong and should I connect to the computer more often and create/edit my playlists this way rather than on the actual phone itself?