The VVT heads swap over just fine, the '07 engine pictured below ran ported Eagle heads with a thicker Cometic gasket just fine with a final compression ratio of 10.75:1. What year is the engine/truck you want to put the supercharger on?
There's a big difference between the pre-Eagle and Eagle front cover. A supercharger from an '09+ (1500 or '10+ 2500) won't bolt to the earlier engine (or vice versa), I tried going the other way with my cog drive setup and it doesn't work.
Here is my '09 VVT front cover with the intermediate supercharger plate
Here is a Procharger from an '09 1500 with the VVT Eagle engine
Here is my '07 non-VVT engine with the 6.1L intake manifold bracket on it, all the holes on the passenger side are used to bolt up the procharger.
The big changes as you can see are the relocation of the A/C and alternator, change in location of the upper radiator hose, tensioner, and all the idler pulleys.