Television theme songs don't really play a role in the lives of Toobworld residents. They're part of the overall universal "atmosphere", along with credits and commercial interruptions, that is experienced by the real world audience. Sometimes their lyrics are quoted by other TV characters and this is either an indication that the character is tele-cognizant (aware of his surroundings as a TV show), or it's just a Zonk that would have to be dealt with.
So the fact that tonight's episode of 'Battlestar Galactica' uses a lyric from the theme song for 'Cheers' isn't of major concern in Toobworld televisiology. Not only is "Taking A Break From All Your Worries" a song lyric but it's also a title, and no one on board the Galactica in Joe's Bar should have any awareness of it.
Besides, there's also no Zonk violation in its use even if Lee or Sam or some other battle-weary Galactican utters it. 'Cheers' and this new version of 'Battlestar Galactica' are part of the TV Universe, but in alternate dimensions. 'Cheers' is to be found on Earth Prime-Time, the main Toobworld, while 'BG' is still wandering through their own final frontier in search of Earth Prime-Time/Remake.