Travelling is no problem between this areas, althow they call the road form Pasto to Mocoa 'trampolin de la muerte' because of it is a small road through the mountains without pavimentation. It is an adventure on itself, but with beautifull scenery.
It takes 5 hours from Pasto to Mocoa in pick-up, in bus 6 hours.
From Mocoa to Pitalito 3 hours, good road with pavimentation.
From Pitalito to San-Agustín it takes 40 minutes.
In case you are interested in staying and visiting some paradises in the nature in Mocoa :
you can stay in the brandnew hostel Casa del Río www.casadelriomocoa.com
You can contact them if you need any information about the region.