Open up Pro Tools as Normal. Once the 'Create Sessions' you will want to go down and click the I/O Settings, which should be labeled as 'Last Used'. You will want to select the option 5.1 SMPTE/ITU as your setup. (Do Not Chose 5.1 FILM MIX, as these I/O settings are incorrect.)
Once the new session is open, Click on Setup in the top Tool Bar and Click the I/O.
If done properly your lay out as of 1,2,3,4,5,6 should as L,R,C,LFE,Ls,Rs.
If this is not set, down below there is a setting for 'Default Format' & 'Path Order'. For Format, have 5.1 selected. For 'Path Order', you will want the 5.1 SMPTE/ITU option selected. Then click on 'Default' to the left of them and the I/O setting will automatically reconnect paths to the correct areas.
Test to make sure
Create a Mono Track and have a active sample placed on it. (Set it to Loop) (You could select an area on the timeline, go to Audio Suite in the Top Toolbar and select signal generator and render a sound to work with.
Once set, click on the Fader icon next to the Output to bring uo the Panning window.You will then have a new window open with a Fader & Black Box Displayed with a green Dot. If you only have the Paner Knob, then your output is not set to the 5.1.
The Green Dot indicates the Position of where the Sound Signal will be coming from. You will also note the 5 Speaker icons on each Corner and top center of the Box as these represent the Speakers that you are using.
While playing the audio, Drag the Green Dot and pan the signal through each corner and side to assure that the signals are coming out the correct speakers.