Finding the Pokemon I want to use

I have name system and I also use the favorites feature in game which really helps with finding the usual suspects for gym usage.

It takes a bit longer when training though, but even then I organize by CP and select all 6 to be lower than the gyms lowest CP defender.

A little of both. I train up gyms with mass (evolve+lucky egg) Pokémon and then transfer them when training team gyms up.

As for taking them down, just use my strongest attackers with move/type advantage and bring nothing else. A lot more worth it to bring Pokémon with high stamina too (i.e. vaporeon, wigglytuff, snorlax, lapras) and use 1 hyper potion healing about 200 HP than bring Arcanine and be forced to use potions and super potions (which run out faster if you try not to waste hit points from heal items and therefore get used up more quickly) like I do.

But, I digress, my main attackers are Exeggutor for the obscene amount of vaporeon in gyms. My vaporeon as it has a lot of stamina and can kill 2 to almost 3 2k Arcanine, or an Arcanine and a snorlax (succesful doging). My wigglytuff as a general stamina buffer, and what ever variance of golem, Arcanine, ryhorn, Random fighting type to round off against what Pokémon are in the opposing gym.