Awesome that you are thinking that far ahead and asking questions...kudos to you. IMHO, I would not mount to the sub box directly for the simple reasoning of direct vibration of internal parts ( I also think about theft, if they take your box...well they get the amp as a bonus as well.) Now, having said that, if you were to dampen the vibration by installing rubber mounting absorbers in between the box and amp would that be an alternative?
There are a few variables here as well. Like, what vehicle (trunk, hatch, truck) that would limit areas to mount to. Also the size and weight of the amp could come into play as well. Under the seat would be nice...but would the amp fit?
Things to take into consideration...power wire length, ground location (ground should be less than 2 feet from amp), cooling of amp, ease of access if needed for adjustments..just to name a few.