Amelia, a lot depends on exactly what you're doing. If, as Jon has suggested, you have multiple takes of a band doing the same song then your first step (as you've identified) is to synch these sequences.
A clapper board is the way to go if you have multiple cameras for a single take but if you've got multiple takes on a single camera it can't help (and as Craig said, it can't help at all if the footage is already in the can :) ).
The way I would normally proceed is to bring all the takes into a sequence and then look at each one at a time. Expand the audio track of both the clip you're working on and the master audio (drag them out, make them nice and big 'vertically'). No matter what the song, there's normally some point that is easily idenitifiable in the waveform - a particular snare hit, a quiet passage followed by guitar coming in - something that makes a nice sharp 'spike' in your waveform. Find the best example of this and move your clip to match this position. Don't forget to lock your master audio track and I'd recommend you lock each video track as you complete it until you're ready to edit. I'd only look at the video to get a rough idea of position initially - lip synching is something best done once you're pretty close in the first place and if your artists are miming to a playback they may not have been spot on in the first place. Don't worry too much if one or two words seem out of synch with the master if the rest is OK - that's just an indication of an edit needed :)
Synch each track in this way until all your tracks are in synch, then save this version and do a 'Save as' to begin editing on a new filename - that way if it all goes pear-shaped you can at least go back to your 'synched' version.
As far as editing goes I always like to cut into something, rather than building from scratch, so I have a 'master shot' - usually a wide of the whole band - which serves as the basis for the whole video then lay clips onto that in increasing 'layers' as it were. So the first 'pass' puts down some close ups of the drums, the second pass the vocalist and so on ad infinitum or until I'm happy with the basic edit. For me, this allows me to keep an idea of tempo and 'exposure' for all the members of the band as well as providing a 'base' to work from visually which I think is important for the viewer.
Personally, I like to make good use of colours and bins to organise my footage and video tracks (all the vocalist shots are red, the drums green, etc.) but how much that actually helps is arguable.
Don't forget that making a music vid (or any video production for that matter!) is a license to cheat. If you've got a cracking shot of the guitarist's head but you'd really like it somewhere else in the song, then just move it! Anything that doesn't give a visual clue to link to the music can be moved and the audience will be none the wiser (and this of course includes facial expressions).
Jon