I came to the series a lot later than most of the bloggers I've seen. As such, many of the early books were already written, and I never really questioned a lot about the order. There were already several super specials and I think I started reading right around when the first mystery came out. (I definitely bought #3, Mallory and the Ghost Cat, when it was brand new.)
But back when I was trying to read all the books in order, I stopped to think about the placement of these books. I felt it was important to read them in order, especially because they often refer back to other books, even the mysteries, that have already happened. The worst example of this, for me, was how they kept mentioning that MA had been in counseling. I had read every book, 1-64 at least part way through and had read almost every book after that, up to 73. (I still have not read #65. We'll see...) I had seen several references to MA being in counseling but never the book it originally came from. Turns out (and I discovered this about six months ago) that it never really happened in a book; the first reference to it actually comes from the BSC chain letter book my mom wouldn't buy me because it was too expensive. It's the secret MA tells Claudia that no one else knows.
Anyway, my sister was making fun of me for having a BSC blog and I was telling her how I couldn't find SS #1, and how I had to read it before I could go on to #10. Why? Because it takes place in summer vacation, before Stacey leaves for NY and Mallory and Jessi join the club. Since school starts in #10, it must occur before then. It also has to be after #8, since it references how MA and Stacey were mother's helpers in the events of that book.
What about the other SSs? I have a few ideas.
#2--Between #24 and #26. Because Emily has already been adopted and Mimi is still alive.
#3--Between #28 and #30. Stacey's back but Richard and Sharon aren't married yet.
#4--Right before book #36. Makes sense, because Aunt Cecelia is introduced in the former and moves in with the family in the latter.
This becomes harder as the books move on and fewer life-changing things happen. There's fewer changes as the books go on and most of the ones that do happen involve Dawn moving back and forth to California. You know, for example, that SS #12 happens when Dawn moves back to Stoneybrook after her "six month" stay in Palo City, but I honestly don't remember what exact book number in the regular books she reappears in. It has to be between #77 (when Dawn is in Cali) and #84 (when Dawn is in Stoneybrook.) Likewise, you know that SS #13 occurs after book #89, when Abby arrives in town, because she's in that one.