Resources like metal, food from fields, and mana from shards just go into a global pile.  I think the only way outposts can help a specific city is by the upgrades (Consulate for population, maybe the Armory and Foritification bonuses). Other than that, the city that an outpost is connected to just provides the build queue for said upgrades and resources.

I assume you are playing Ceresa/Resoln if you are getting elemental creatures from shards?  They get stronger as they level up.

outposts and resources are always connected to and produced by the nearest city, you cannot change that.

It's because of the faction trait "Binding". You get better creatures if you upgrade the shards, but even the early ones are very good to keep pressure on an enemy and to scout the map.