You should put it however it makes the most sense to you. I like to separate ongoing bonuses from things that require active use. So for example, the toughness feat would be kept separate from power attack. Touch attacks from cleric domains would go with the "weapons" section. Put it wherever it makes sense for you. That's why I prefer to make my own character sheets. It works better with my brain because I know how it works.
The entire point of the sheet is that it lets you remember what you can do. And maybe the DM if they're doing an audit.
You don't really need to do class abilities unless you're taking an archtype... you're a druid level x, every druid level x has such and such abilities.
Should I put only my class special abilitys in the special ability section on the character sheet?? I realized when I started adding every single ability it starts to get crowded(racial traits, Pathfinder society faction traits etc.)
I would say, if you're super new to the system and this is your most pressing question, you're doing pretty well. That section is typically just to help you remember stuff that you need to keep track of. I know I forget racial abilities completely unless I have them right in front of my face.