I've been a faithful Spidey reader since early 2010. Every issue of Superior just keeps getting better and I can't wait to see how Goblin Nation plays out.
Carly met Pete while he had Ock's body in Amazing #700, Pete tried to tell her that it was actually him, and that thought has been nagging at her since. She's slowly pieced everything together.
Carly knew Pete was Spider-Man because he told her at the end of Spider Island. Roughly Amazing #674. She broke up with him right after.
Shortly after that, Carly started hanging out with MJ. They've become best friends since, using Pete's secret and their failed relationships with him as a bonding point. Roughly every few issues starting in Amazing #675.
Yes it is still good.
Depends on when you want to start. Dan Slott's run (more or less) started with this :
[ame]http://www.amazon.com/Spider-Man-Big-Time-Ultimate-Collection/dp/0785162178/ref=sr_1_1?ie=UTF8&qid=1392949267&sr=8-1&keywords=big+time+ultimate+collection[/ame]
Amazing Spider-Man 648 - 662, 654.1
Then continued with :
[ame]http://www.amazon.com/Spider-Man-Time-Complete-Collection-Volume/dp/0785185402/ref=sr_1_2?ie=UTF8&qid=1392949267&sr=8-2&keywords=big+time+ultimate+collection[/ame]
Amazing Spider-Man 663-677, Amazing Spide r-Man Infested 1, Free Comic Book Day 2011, Spider-Island: Deadly Foes 1, Daredevil 8, Spider-Island Spotlight
A few of the plot points that confused you started up here. I admit, this is a little bit of a ways back in regards to Spidey, so if you want to start with Superior, you can go with :
[ame]http://www.amazon.com/Superior-Spider-Man-Vol-Marvel-Now/dp/0785185216/ref=sr_1_5?ie=UTF8&qid=1392949389&sr=8-5&keywords=superior+spiderman[/ame]
That includes Amazing Spider-Man : Dying Wish (#698-700) and Superior Spider-Man Volume 1 (SSM #1-5)
There are also four paperbacks available, and Dying Wish is available in paperback form as well in case you don't want the hardcover.