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The way I've been doing, and I'm sure SOMEONE here has a better way to do it is I do all the Attribs first and then do traits and assign skills ETC then do my morph stuff and come back and make all the adjustments in the end. I love the system character creation is a bit clunky and time consuming, I dont mind though it really defines a character before you write any backstory.
Mandatory Flow Chart
1)Ego stuff
-Attributes
-Traits
-Skills/Knowledges
2)Assign gear CP
3)Customize Morph
though I guess if I already knew what I wanted my character to do I would customize the morph first to get any bonuses to attributes already in the pool instead of mucking around with it on the back end.