Hi,
I'm a newbie as well, but i may be able to help. Not sure why it went a bit random on you, but if you only have trial versions of the software, you will have limitations of gcode etc. this goes for lazy cam also, if you have the trial version, you can't specify offsets to choose which side to cut for instance.
in response to your questions-
It only matters as to which is better for the job
Each time you click optimise, it changes the route
It doesn't seem to matter when you do the layering.
hope this helps, let me know if i can be of more assistance.
aaron.