Hi Slabbacks - sorry for the late reply, most RM talk now takes place on our dedicated forum
here, so please do drop in. We went over to our own forum because we have so many Lowrance users now, it didn't make sense to stay on a dedicated HB forum.
In answer to your question - just go ahead and add tracks to your project as you record them. Any editing of the track (eg to remove bad depths) will be reflected in the project, so you don't need to do things in a specific order. You might find that bad depths get averaged out anyway in the project.
Matt