I have a friend that spends nine months of every year in Ecuador just using the T-3 and the 12-IV visas. Here is what he told me. If he enters the country on a T-3 on June 1st, 2014 he’s good for 90 days. He waits until near the end of those 90 days to get his 12-IV which gives him an additional 180 days. So he would be able to stay in the country until approximately the end of February 2015. At that point he needs to leave the country but is able to return on a T-3 visa one year from when his last T-3 was issued, so June 1st, 2015.
He has done this for several years now and not had any problems with immigration. So, theoretically you should be able to come back to Ecuador as soon as November of this year. I can’t guarantee that you won’t get an immigration officer who has a different understanding of the time limits on these visas, but most likely you should be just fine in re-entering Ecuador in February of next year.