I believe the rules are that the 90 days starts when you start the trial account.

I played the trial account for 2 days before I wanted to transfer one of my 70s over to the new second account. When I looked at my billing, it basically started my "free 30 days" from buying the copy of WoW, after the 10 free days, so I didn't lose any of the 10 free days from the trail account.