Having the same troop in multiple teams has no effect on anything.
In the PVP menu, you can select “defenders” and then choose one of your teams. That team will represent you in all PvP defences.
Others have suggested being able to reorder the teams in your list, but right now, there is no way to do that except to manually rebuild your teams in the order that you want.
You have a maximum of 20 team slots, but there are more than 20 kingdoms, so it is not possible to make a team for every kingdom. Personally, I have a couple of kingdom-specific teams that I keep on my list, but if I need a specific team for a particular daily task (I am on PS4), I have a couple of slots that I keep for task teams and change them around as I start new tasks.
Adding a hero to a particular team won’t have any effect on any other team with your hero on it. When making your team, you are essentially recruiting the hero’s weapon rather than the hero itself. However, if you change your hero’s class in the hero menu, that would affect any team that has a hero on it. So, your weapon and hero bonuses might work on one team, but not on another. I’m not an expert on the use of hero classes, though.
If I am experimenting with teams, I usually try them out in Challenge mode in a specific kingdom. That allows you to try the team out at different levels of difficulty against different types of teams. You don’t get a lot of rewards for that, but you don’t lose anything except your time if the match is lost or even if you are halfway through a match, realize it isn’t working and just retreat to change your team around.
Hope that helps!