So I suck at FFH...

As Sidar there is no problem with having them both in the same city. You can get all the multipliers in one city (capital) without issues... e.g., Crown, academy, bazaar of Mammon. Especially since you have the extra hammers from your settled scientists, you might as well build the gold buildings in the same place.
 
Yes but it saves time building (because two cities can do it at the same time).
 
Although, if I'm not running God King, making the capital my academy city isn't that bad since it doesn't have any other multipliers, right?
 
Before building the academy it's probably a good idea to decide on city specialization. If you have a city with decent amount of food tiles (flatlands that can be irrigated) and hills (5-7) then it can be a good military production city. Building academy there would be a waste. City with high commerce potential is a good place, although city with lots of food can be great too (sage specialists + aristograrian economy).

Basically, just pick a military city (city with enough hills and farmable tiles to actually work the mines) and don't build your academy there.

On the other hand you'll get more sages later so you may just as well build academy where you have most commerce now. After all, AV shrine (if you can get one) is good for both science and military cities.
 
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