There at least a couple of threads on this very issue, however I will save you the search.
One of our main products for the military is made from 6061 and over the last year I have experienced more than a fair amount of pain getting this correct. In the process I brought in 5 CWI's, two of them SCW's and two Weld Engineers. It all came down to contamination and technique.
If you have dirty 6061, you have two choices: a) Get cleaner aluminum or b) Clean the aluminum in Bio Circle Alustar 100. We use a tank with an agitator and heater. We hang the parts in the bath for a couple of hours. This also works well for cleaning reworked weldments before repair.
Bag the parts to limit the reformation of aluminum oxide as much as possible unless they are going directly to weld after drying.
When ready to weld, wipe the joint areas with Arcal Weld-O cleaner, then wire brush in ONE DIRECTION ONLY. Brushing in both directions encourages oxide to form. Pratt and Whitney uses wire brushing in both directions to cause oxide to form on jet engine parts. Do not use power wire brushes...that did not go well for us.
Some additional points:
Do not run the parts through an abrasive deburing machine as it will create grooves that hold dirt and makes it MUCH harder to clean. Hand debur edges.
Do not grind carbon steel in the same end of the building that you are welding aluminum. It WILL contaminate the aluminum and create nightmares with the finished welds.
Ensure that your MIG and TIG fill are in sealed containers. Use only good quality fill, not fill purchased from companies that buy up excess and respool it for resale. Cover the spools on the machines when not in use.
Watch out for CRATER CRACKS. Check a good size sample of the welds under 10X for crater cracks. Ensure that your welders terminate their welds properly. Turning the TIG cup away too soon at the end of a weld or poor MIG technique will result in nightmares, from crater cracks to throat cracks. If they are not using a crater fill setting, ensure they are filling the crater.
Feel free to ask more questions if needed and I can point you to some very good websites such as:
http://www.thefabricator.com/author/frank-armao