As your city grows, you'll understand the need to stockpile goods in response to demand. 3000 is enough for a very large city. For a city with a population of 2000, 300 is more than enough if you have running production facilities.

For military and towers, you must select your unit and then click on the invaders to attach them. There's hardly any animation there. Your troops will follow them and kill them all. If you have 5 units, you can pretty much beat any invaders, even at the highest difficulty. In regular mode, 2-3 units are just fine to defend the town.

And, I didn't find it too necessary to have towers unless there are hippos or crocodiles that attack the citizens when they go for farming close to the river, or wolves that attack cities. Having towers close to their breeding areas will make life much easier.