A nice work flow is to do a save as at the end of the cue you've just worked on and name it for the next cue. Delete all your regions in the newly created project, and the rest of your Channel Strip settings are alreay in place and you are ready to start working on the next cue once you set the new smpte start time. You can even save it to the same project folder. That way all your cues/projects will access the same pool of samples and audio files, in case you re-use some from cue to cue.
Freeze renders a temporary 32 bit audio file comprised of the data that is on the track that's frozen. It saves cpu resources by freeing up demands for the heavy processing that might be on the track that is being frozen (if it uses lots of plug-ins. But it also places greater demands on the hard drive throughput, since it is now reading a 32 bit audio file. So, it is better for cpu mileage, but harder on the hard drive. The conventional wisdom is to only freeze tracks that use a lot of plug-ins, and only do it if you are reading/writing your audio files to a separate drive. Protect merely protects regions from accidentally being edited on the tracks that are "locked".