Also, do you guys always use the jobbers we win by playing the story to upgrade any Super Rare and up characters?
Well, it depends. There's sort of loose tiers that units in
Treasure Cruise fall into. The question comes up somewhat often, and despite the top post having much of this info, I've been wanting to type my own TL;DR version of the answer:
At the bottom, there's basic units with generic names, like "Fighter Group Cabin Boy" (probably what you mean by jobbers). These groups are often made up of same sprite, painted different colors. You can use them to level up rarer units early on, but at advanced levels, you will usually sell them, as they aren't nearly as cost-effective for leveling as "Booster" units. In some rare circumstances, however, these characters show up in teams, often as substitutions for units you don't have, such as STR Giant instead of Arlong or Kidd, or QCK Baroque Millions for Lulu.
Then there's units that usually drop only in Story Mode, such as Laboon, PSY Enel, and INT Brogy. Some are minor characters, but as the story goes on, major characters start to show up. Some of these units are really good--especially villains such as Crocodile. Most are mediocre, and some are terrible. Some of the earlier story units also had dedicated fortnights, such as Alvida and Kuro. All of them, even the crappy ones, can be exceedingly difficult to collect, due to a cruel RNG that dictates the drop rates. On rare occasion, are events where certain story-only units are available in Friend Point Recruit. These events are the number one reason to save Friend Points.
Next are units that drop in fortnight events, such as QCK Kaku and DEX Perona. The end bosses of these stages tend to be solid units, with decent HP and damage, while the mid-bosses can be anything from useless to essential. The exception is mid-bosses that randomly appear, such as Kimono Nami or Paulie. These tend to be above-average units, often superior to the bosses themselves. Most mid-level teams are primarily comprised of fortnight units.
Raid bosses typically show up for 24 hours. They are always strong, high-cost units, and typically powerful captains, such as DEX MIhawk. Some are essential to success, especially when used as stepping stones to take down other raid bosses. High-end teams almost always have one or two of these.
Rare Recruit exclusive units are some of the best available. This group includes legendary 6* units such as Strong World Shanks and Whitebeard, which, properly used, stomp most of the content in the game. However, some characters you will get from Rare Recruit are
not exclusives. It also contains the basic Straw Hat Pirates, and all their potential evolutions--Hot Rock Stew Sanji, for example. There are also early story/fortnight units in there, such as Don Krieg, Arlong, and the dreaded Chore Boy Coby.
Beyond that, there's Evolver units, such as seahorses and crabs, and Booster units, such as turtles and pigs. These units are saved for improving rare characters, and rarely fielded. There are promotional units that show up directly in your inbox, such as Chopperman, but Global hasn't had many of these. From time to time, they also give away existing units in promos, such as extra base Straw Hats. There's also a few units that are primarily found in Friend Point Recruit, such as Yosaku and Hiking Bear. In Japan, there's Colosseum units, but those won't be hitting Global for a while.
So, in my opinion, the best plan of attack is this: Save unique story and fortnight units, especially ones with Captain Abilities, Specials, and secondary evolutions, at least until you have a better grasp of the game. Figuring out which ones are junk takes experience, and as long as you steadily upgrade your character box, you shouldn't have storage issues for a few months.
Always save any duplicate Straw Hat pirate. You will want them when version 4.0 lands--especially Zoro and Luffy. It's okay to evolve them to fill out the slots in your character box. If you get an extra Sanji, evolve him to Plastic Surgery Shot, then keep him around, to evolve a certain raid boss.
There are also a few units you will
not want to evolve, at least not until you have a duplicate. The most notable ones are Streaming Wolf Swords Zoro, Mirage Tempo Nami, and Golden Pound Usopp, or anyone else that loses a powerful special upon evolution. Also, if you get a 4* Rare Recruit exclusive that evolves into a 5*
you already have, and evolving to the 5* form would give the unit a cost
higher than 20, I would definitely consider keeping the 4* duplicate around. If you get Sengoku, who boosts any character with a sub-20 cost, a collection of such units can form powerful teams few others can use.