ANIMORPHS was an equal collaboration from the start. But that collaboration started much earlier.
Part of the confusion came because we were actually not just two different writers with two names, we were two writers with 11 names. Beth Kincaid, C. Archer, Pat Pollari, Katherine Kendall, Nicholas Stevens, Katherine Michaels (heh), A.R. Plumb and others we can't even remember. Actually "Michael Grant" is yet another pseudonym -- it's actually Michael Reynolds.
Neither of us could even begin to parse out who did what and when and why.
The reasons for pseudonyms are various. Our first book was for Harlequin which in those days (early pleistocene) took ownership of the author's name. So: pseudonym. Then for a while we were ghostwriting for Francine Pascal, so another name. We worked for Disney for a while and we were writing so much of their list it was embarrassing to them, so they asked us to conceal the extent of our involvement with various pseudonyms.
Are you bored with this answer yet?
And then there was Barf-O-Rama. A sort of self-evident excuse for a pseudonym. Meanwhile, just to make things more complicated, Michael was writing for newspapers as "Michael Robinson."
Then we went into YA romance with OCEAN CITY and BOYFRIENDS/GIRLFRIENDS and Michael really didn't want to have his name associated with the writing of breathless make-out scenes between teens. Because "Eeww." Neither did Katherine but too bad: someone had to take the blame. We wrote those as "Katherine Applegate."
By the time we started ANIMORPHS "Applegate" was a semi-established name as far as publishers and bookstores were concerned. So it made sense to stick with it. We thought about using two names, but it makes it hard for readers to remember. So, no.
We assumed we'd eventually use Reynolds or some Reynolds-esque pseudonym because of course we didn't know ANIMORPHS was going to be 63 books. We figured six or eight and off we'd go to the next thing. But of course ANI spawned EVERWORLD and REMNANTS.
Then we quit.
Then we ran out of money so we un-quit. But enough time had passed that we didn't see a huge advantage in "K.A. Applegate" as a name. Katherine thought quite a bit about dropping Applegate altogether but in the end decided to keep it. But we were no longer interested in writing together. Katherine wanted to do younger and/or more literary stuff. Michael wanted to do GONE. The writing partnership ended upon quitting REMNANTS.
That being said, of course we talk about work all the time. We bounce ideas off each other, we help each other work through POV or plot questions. We just write different things.
The best we can tell you in terms of who did what is: if it was lyrical, descriptive, or romantic it is slightly more likely to have been Katherine. If it was violent, political or funny, it is slightly more likely to have been Michael. But even then if you guessed a particular scene you'd probably be wrong -- and god knows we wouldn't remember.