The permutohedron P4 is the 3d truncated octahedron. Its facets consist of 6 hexagons and 8 squares.
The permutohedron P5 is a 4d polytope with 30 3d facets: there are 10 truncated octahedra, and 20 hexagonal prisms (I believe).
The permutohedron P6 is a 5d polytope with 62 4d facets: there are 12 P5 polytopes, 30 truncated octadedral prisms, and 20 polytopes with 36 vertices. These latter seem to be 4d polytopes with 36 vertices and 12 3d facets, each of which is a hexagonal prism. Is that correct?
The permutatopes $P(n)$ are just the omnitruncated $n-1$ dimensional simplices. Accordingly these are represented by the Coxeter-Dynkin diagrams $x3x3x3...3x3x$ with $n-1$ nodes and in here each node symbol $x$ represents a ringed node (in a typewriter friendly way).
As is known for Coxeter Dynkin diagrams, the according facets are obtained by omission of any possible single node each (as long as those do not become degenerate). I.e. in here we have $$\begin{array}{ccl}.\ x3x3...3x3x & = & P(0)\times P(n-1)\\ x\ .\ x3...3x3x & = & P(1)\times P(n-2)\\ ... & = & P(k)\times P(n-k-1)\\ x3x3x3...3x\ . & = & P(n-1)\times P(0)\end{array}$$
The respective counts each are provided by the $n$-th row of the Pascal triangle (excluding the extremal 1 each), e.g. the truncated octahedron $P(4)=x3x3x$ has $choose(4,1)=4$ hexagons $x3x\ .$, $choose(4,2)=6$ squares $x\ . \ x$, and $choose(4,3)=4$ more hexagons $.\ x3x$.
As for your question about the 5D $P(6)$ this esp. provides $choose(6,1)=6\ P(5)$s, $choose(6,2)=15\ P(4)$-prisms, $choose(6,3)=20\ P(3)$-duoprisms, further $choose(6,4)=15\ P(4)$-prisms, and further $choose(6,5)=6\ P(5)$s. Here $P(3)$ clearly is the regular hexagon. Thus those 36 mentioned vertices of yours indeed divide as $6\times 6$ within these duoprisms.
--- rk