You can go to Terminal Norte (also called terminal Carcelen). All taxi drivers know where this is.
(There is only one direct bus to Cotacachi, I am told — I can’t verify its existence as I’ve never taken it. It leaves some time around 5 am in the morning.) The buses to Otavalo run every 20 minutes or so. Buy a ticket for $2 at the window and they will also charge you 15 cents for a terminal fee. If you take luggage, watch them stow it and be sure you keep an eye when passengers depart that they don’t claim your luggage. Not to worry, the likelihood of this happening is small. But it pays to be vigilant. If the bus is full, don’t put your stuff on the floor or overhead, but hold it on your lap.