Generator Power Inlet Box location
That plan looks fine and normal. They don't like top entries because real-world, they leak. 

I myself prefer a "drip loop" as it were, where I enter the bottom of both boxes, with an LR and LL right next to each other.  

You must use something like #8 THWN wires.  You can't use NM-B obviously.  And you cannot use #6/3 UF-B, because UF-B is thin and wide, and that requires wide conduit... 2" for #6.  And that inlet box is absolutely unable to support an opening that large! 

Generally for 1 cable in conduit, the conduit's practical ID must be 138% of the width of the cable.  With 6/3UF that puts you at about 1.65 inches, too big for 1.5".