Ok I want to use one of the economy systems that are on Bukkit (iconomy being considered here though open to suggestions), but I have a couple of questions first. How do players initially get money as this is not part of minecraft? Do I give them an allotted amount to begin with or what? Do they trade with just players or with npc's when they are available in minecraft 1.9? Hope someone can help me out as I dont want to implement something half heartedly.
usually this is set in the settings of the respective economy plugin. that totally depends on how a plugin makes it, read the documentation. It is usually implemented with commands. 1.9 isn't out yet so we can't say anything about that.
i like to use: iconomy, giant shop, giant shop location, and sign commands. i can allow my players to have money, then i create shops with various tools and materials in that players use signs to shop a., i also use cookiemonster to set money drops to mobs. this way players can trade money with each other via iconomy, can buy with a global shop via signs in stores, and can get money by harvesting /selling things and killing monsters. whenever i can find a suitable player owned chest shop plugin that will work with iconomy ill add that as well. hopefully this helps you get yours set up.