Well, Amazon Backpackers (I think that's who you mean) has been a reliable agency for many years, but if those tripadvisor reviews are truthful, it sounds like there have been some problems. And I expect there's still going to be some residual World Cup craziness through the weekend as other attendees take their jungle tours when the matches are over.
Now that I understand how you booked, there's nothing unusual about booking through email and paying cash when they pick you up at the airport--that's how most of them work--but as you say, you aren't under any obligation yet. Do check out the three agencies I mention (and there are several other reliable ones, too, that I haven't toured with personally)--you can wait until you get to Manaus to make a decision if you prefer, but I like getting that airport pickup included. If you decide to wait, only buy a tour at an office (or their rep at a special desk in your hotel/hostel; sometimes they'll even send a rep to your hotel), not from someone who approaches you in the airport. On the other hand, legit guides may see you at the airport while they're there picking up other tourists and suggest you go to their office in central Manaus--that's OK, too.