Joy,
You are right, there is so much to this program that you can overwhelm yourself very easily. When the hybridizing section was greatly improved, I went bonkers and entered every pollination through seedling, and got myself totally confused. Now I wait and just enter the potential keepers. The garden map feature has been a real help (as long as I remember to move the daylily in the program when I move it in the garden). Now I usually locate a seedling or a registered plant pretty easily. Key factor there is having a plan to start with. Name the garden/bed, number the row, and number the plant (and remember which end of the row you started on).
This is by far the best program I have found. I'm not the guru for it, but if you have some questions i"ll be glad to try and help. And, BTW, Kent Belan is one of the best at helping with problems.