I had the same issue....until I saw that the Secret Avengers saga, takes place entirely before the New Avengers tale. (There's a note at the beginning of each Secret Avengers, letting us know it's before NA)
You even see the crew, Beast, recovering War Machine, Etc in NA....picking up where the just finished SA ends....
Hope this helps!
I haven't brought the last couple of issues of New Avengers because I thought its being all about the Phoenix's past history with the Iron Fist which doesn't really interest me but I'm sure none of the crew in Secret Avengers appeared in those issues.