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Hello Lucas
I recommend you take a look at this Composites Playlist
https://www.youtube.com/playlist?list=PLGNemB0NFb0BcNU7CMkFcgrGRBVGMrwPj
And our help
https://help.altair.com/hwdesktop/hwx/topics/pre_processing/composites/composites.htm
Here are some guides to your questions
For your first question, the basic difference is ply based vs zone based property.
Or optimization, when you are running topology it doesn't make sense to include plies (pcompp). You are just looking to get load path (initial design). Ply based optimization would be part of the fine tuning application.
Thanks
jason