As a general rule, you want to try and pump most points into the stats for the tree you are going to use, and those stats include the Accuracy and the Damage.
For SPY you get your accuracy stats from the attribute: Perception, and your damage from the attribute: Reason.
I'm not sure which manual you are reading, but since we have had a combat revision done a while back, the old manuals are good for 1 thing, keeping an open fire burning.
As for the green effect? I'm a bit lost on that. Is there a particular ability you are using? My suggestion is to try the moves ingame and that will be the best way to learn what you need to do and what each move is capable of.
If you are interesting in the Master Knife Thrower tree, here is a guide made by the staff of MegaCity Times, that should help you understand a few things (Plus is CR2 compliant).
Ah, I see.
Yes the Green circle shows in the ability when it hits. Might I suggest 2 guides written for CR2, read these, you will understand a lot, very quickly.
Cr2 - Beginners Guide Introduction to Cr2
Both have images to explain things more clearly, too.