If the checkbox for Manually manage music is checked on the iPod's Summary settings screen in iTunes, your iPod is currently not using automatic syncing. Here's how to removes songs (and other content) manually.
Select the iPod in iTunes (click its device button on horizontal bar) to show its settings screen in iTunes window. Along the left side (in the sidebar), under On My Device, select Music. To the right, the iPod's song list is shown. Select a song you want to remove and press Delete on the keyboard. You can do this with more than one song selected at the same time. If you have other content to remove, such as podcasts, in the sidebar, select that category under On My Device. And do the same thing.
Keep an eye on the Capacity Bar at the bottom of the iPod's settings screen. Once you have enough free space to fit those audio files, you can try manually adding those files again.
NOTE: Not sure what you are describing about playlists, but IF the iPod is set to Manually manage music, removing playlists from the iPod definitely will not remove the songs. Songs can be on the iPod by themselves without being on any playlist. So, removing the playlist just removes the playlist. The songs stay on the iPod.
If you want a better way to manage what is on the iPod, you should set up automatic syncing using playlists to select what is loaded on the iPod. Then, when you want to change the iPod's songs, you can just update those playlists (in your iTunes library) by adding and removing songs. The iPod does not need to be connected. The next time you connect the iPod, iTunes automatically updates the iPod with the same changes. If you want more info on how to set this up, please post back.