Ako my morrocan trip was a DIY thing lang. The train system in Morocco is superb and cheap! Very easy to go from one place to another. Take the special though para may sarili kayong train car, not too different naman sa normal fare. Also the taxis are also mura ang kaso ang luluma at dumi ng taxis nila, haha sabi nga namin nung friend ko, yung tinatapon na kotse na 19 kopong kopong sa pinas ginagawang taxi dito hahaha! Yung out of the way places though, like VOlubilis, you need to hire a taxi. Just look sa internet ng going rate ng tours ( usually 3 hours sa VOlubilis, iintayin ka ng taxi driver doon sa entrance habang iniikot mo yung ekta-ektaryang roman ruins). To be honest, I have never taken package tours in my travels hehe, pero I researched before traveilling, for me it´s part of the enjoyment eh, the checking out of sights to go, food to eat, etc. I spent 3 nights in a traditional dar (centuries old structure turned into traditional hotel) in Fes, and it was a great experience, the rest I stayed in Ibis hotels na haha. I also booked sa isang top rated moroccan restaurant (actually home restaurant sya, it´s a three story century old house that the owner converted into a restaurant, yung first two floors naging restaurant, the third floor bahay nila) just to experience yung best moroccan food I can afford. Masarap ang tagine and yung chicken pies nila. And the ever present mint tea. For the Medina at fez though you will need a guide to navigate its labyrinthine streets, also so you can go to the top of the leather town. Kasi ang mga local guides my connect connect na eh, pero do note na every stop you make, syempre itatry ng mga sellers na bentahan kayo (carpets, ceramics, argan oils, leather items, sweets, traditional djellabas) but wala naman silang magagawa pag sinabi mo na NO eh. hehe.
I did not go up the Atlas mountains though so our other sisses might have recos on how to go about that, but I imagine you can just use the internet to make arrangement beforehand. Cheers!