I am currently levelling my SMN to 50 so far I just hit lvl42 and my rotations are like this

For single enemy

Bio, Bio 2, Miasma, Virus, Atherflow, Fester, Ruin 2 and repeat

for group of enemies

target marked mob

Bio, Bio 2, Miasma, Virus, Atherflow, Bane, Tri Disaster and Fester with a Ruin thrown in if time.

As for my pets, I'll be honest I let them attack the mobs and leave them to their own devices, ill heal as and when their hp gets low and I just recently aquired Rouse so that will be incorpareted shortly