I have read and seen different approaches to mic placement (cabs laid on the ground with the mic pointing straight down 1/2" off the ground). This shows what I am talking about :-

I would like to find out a little more about the 'correct procedure' but here is what has worked very well for me.
To date I have always had the mic on axis roughly at 10-12 feet away from the cab being measured
This is the method I use for the Behringer DEQ and measurement mic:-
1) Set up your PA system, only plug in one side of your tops.
2) Place the measurement microphone on axis pointing at the top cab roughly 10-12 feet away from the cab to allow the elements to integrate
3) Reset your eq on the DEQ flat
4) Press the RTA button and the screen will say 'edit target curve'. The unit will show you the 31band eq but only down to 100hz - It should be completely flat - don't change this curve
5) follow the on-screen instructions and the unit should then start its process (you may have to press 'start') No need to have the pink noise at war volume, just loud enough to get over the ambient room level. You adjust the level of the pink noise by turning the large central control.
6) Press the page button to view in real time the adjustment being made to the graphic. At first the unit will start with massive changes by grabbing 3-4 eq sliders at a time and making big adjustment, keep watching it and it will start to re-adjust the eq and then start to adjust things less and less. Once it looks as though it is only making tiny adjustments you can press 'done'.
7) press the GEQ button and you can see the adjustments that have been made. Every time I have done this there have been several single freq's that have been boosted/cut massively. I will tend to smooth these out as I make an assumption that they could be room related modes
8 ) Plug your subs and tops back in. Play some music through the system and try swapping the polarity of your subs or tops over. One will result in stronger bass end at the crossover freq. I always check this out at each and every gig as sub placement will dictate how this effects things - typically my subs are inverted
9) Listen to the music with the eq on and then bypassed, you may need to adjust the overall EQ gain by a couple of DB's to make up for overall eq loss due to cuts being made in the eq shape - I simply listen for the volume difference and adjust to suit.
10) Don't rely on the RTA result being the complete answer.....you may find that too much has been cut from the lower mids for example...adjust it to suit, but in my experience it has always resulted in a far, far better sound.
Hope that helps a little
Dave