Cleaning Technique & Experience
Yes, it will take a few times before you get onto the technique of cleaning and using a wand. Happens to all of us when we are starting out.
First, your system is operating just fine because as you have indicated, the recovery water was "dirty". And, that would indicate that your system is powerful in regards to extraction performance(we all ready know that)
I would think that if you "Pre-Sprayed" the carpet, or particularly, the high traffic areas, let dwell (approx. 10 mins+-), then hot water rinse, then this will be a good beginning.
From here, it becomes "wand technique". Your wand is 12" wide. On very dirty areas, move the wand --back & forth-- in a straight pattern, approx. 2 1/2 foot stokes, while spraying in both directions. Concentrate on this area (12" w x 2 1/2' L) while flushing out the dirt/grim. When you feel it is clean, turn off water flow and take a few extra dry strokes. Then, move wand over to the next area (12" w x 2 1/2" L)
The more you do this the better technique and experience you will acquire.
However, never forget that you cannot preform miracles either. Worn areas or sometimes what we preceive to be "dirty areas" will not always come out looking as a "clean-clean" appearance because of other factors involved.
Hope this helps!