You can select which type of marker to drop as well. Hitting insert just drops a generic marker. There is a marker toolbar that you can use that calls up a marker dialogue box. From there you can select cd markers that snap to quantization points for perfect boundary sections. You can also name the markers there, or auto name. Right clicking on the marker heads will also bring up the dialogue box. If you use the cd markers (red heads) you don't have to save the whole file as in with generic markers (blue or yellow heads).
I track the whole file out using cd markers and name with .flac naming convention. Then, I go to the file>new>cd project and add the whole wave file. It then tracks it out for writing. Select cd>save all tracks as individual files in the directory of your choice. From there, you can burn the cd and when done, open flac frontend or shntool and drag/drop the individual tracks for compression/archival purposes.
Make sense? I am away from my home computer so some of the commands may be off by a smidge. But, you should see what I mean if you mess around with it.