My sewer line comes out of my house for 6 feet than 90 right and straight to main for 60+ feet(where it goes under a large fir tree). I have roots growing through my line(6" red clay pipe), I need to know should I put my clean out before the 90 or after since the clog is only in the straight section of pipe?

Typically, you'll install the cleanout so it is about 18" off the foundation wall...this way the lawn mower can't hurt it and you can keep it up high enough so it won't get buried.

You should also consider starting a FOAMING root treatment such as ROOTX... check it out at:

RootX is the simple, effective and proven solution for sewer root control (http://www.rootx.com/)

Good luck!

Mark