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I have a 6.0 with a L76 heads, FAST 102 intake and Holley Sniper throttle body
I have the valley cover with the vacuum port on the motor (I also have the valley cover without the port setting on a shelf in the garage)
My throttle body has a vacuum port and so do both valve covers
My question is what goes where
Do I use the valley cover with the port, or the one without the port
Added a couple of pics
Do a search for PCV diagrams. One or more of them should apply to your situation.
There should be two vacuum ports on the TB. One before the blade (fresh air supply) and one behind it (crankcase fume intake).
Many I've seen pick up air from the front of the TB, go to one valve cover, then a line goes from either the valley plate or the other valve cover.
Depends on the year of the engine in question
Basically, you pull fresh air into one valve cover and suck the fumes from the other one or valley cover. Put in PVC diagram or crankcase ventilation diagram. Use Google and enter LS engine PVC. I guarantee something will come up.
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Vacuum/PCV??? 
