Feeders wires to sub panel in garage with generator wires to main breaker box in the house in same conduit
Sounds like you're doing everything right and side-stepping the usual mistakes we see in this arena.  

Well, I can tell you the derating part.  You'll have 4 live conductors (neutrals and grounds don't count for derate purposes). There are 3 columns in Table 310.15(B)(16).  You must use the lowest temperature that both the wire itself and the terminations (connections) can bear.  For instance if you have a 75C lug on the breaker and THWN-2 wire good for 90C, but your generator inlet is 60C rated it drags you down to the 60C column for your practical load (e.g. for #6Cu 55A rounding up to 60A). 

However, when you derate, you derate based on the highest temperature the wire is possibly allowed.  So that's 90C for THWN-2, for #6Cu that is 75A.  

With 4-6 wires (that count) in the pipe, you derate to 80% (but off the max the wire is allowed).  80% of 75A is 60A.   

Why don't you derate off the 55A number since you are terminating on a 60C lug?  Because the 60C lug is not inside the conduit. 

NM-B and UF-B cables have an exception.  They are 60C wire through and through. But  you are allowed to derate of the 90C column anyway.