I will try to sum up what I understand as best I can, anyone out there correct me if I am wrong on any of these points.
First, there is a difference between foreign trade routes and resource trading. Trading with Isabella to get clams gets those clams for any city connected, via roads and rivers to your capital.
Trade routes are created for each city, up to the limit that city has (different civics, techs, and buildings can increase the number). The trade routes are calculated, as I understand, from most valuable to least valuable depending on what a given city is connected to, again via roads and rivers. If you have those five cities, all of them interconnected, but not connected to any foreign city, each city will select trade routes starting with the most valuable, probably your capital.
If each city has three available trade routes, the capital will connect to the three most valuable cities, the second most valuable will then have two trade routes to connect to the next most valuable cities, etc. The fifth city though, won't be able to create a trade route with your other cities however, because all of the other cities have used up their available trade routes, and so will have no active trade routes.
The complex calculations in the other posts calculate how much commerce you will receive for each trade route.
I hope this helps some.