Buying the song from Napster will give you a song that is still in a format that is not compatible with iTunes or the iPod. But after buying it you should be able to burn the song to a CD. Once you have it on a CD, you can then use iTunes to rip the song into AAC or MP3 format and put it on your iPod.
Many people find it easier to buy the songs from the iTunes Music Store instead of Napster. The price ends up being the same and you don't have to go through the trouble of burning the songs to a CD and then re-importing them into iTunes.