Some bikes are better than others, like my 12R v 10R for comfort over distance is the difference of a sore butt compared to a being a cripple at the end of the day, suspension settings and bike gear play a part too, i.e. wearing racing gear doesn't make for a comfortable day compared to touring gear IMO..
Having more saddle time over a few weeks helps build a tolerance.
Plan your ride and stops well, look after your body with keeping hydrated and the right foods, this lessens overall fatigue which will make you less susceptible to soreness.
I find shifting around on the seat to have different pressure points in contact helps.
In the corners I dont notice it as my mind is busy and shifting in the seat a bit anyway, on long straight empty roads I often sit almost off the seat and dangle my leg which also helps for leg soreness but if you feel thats dangerous dont do it.
Every 2 hours or so after refueling I might do a few stretches, walk around, and lay down flat on a picnic table at a park and let my legs swing (sounds wierd but it works).
I have an airhawk cushion, very nice, however it wont stop your arse getting sore just delays it by 2 hours, it makes the seat higher and feels like you will roll off the seat a bit. So I normally have it stowed away for when I really need it like late in the 2nd day of 6-8hrs in the saddle
All the above works for me and may not be what others do.
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