How does Cache work?

That's... a lot of questions. Probably should have a few of those separated off into their own questions. Also, the term 'Cache' is used for two different things, so I'll see what I can do to separate things.

Cache (the resource) is basically what it sounds like; cash. It's the main form of money in Saint's Row IV. Cache (the menu option) is where you go to get your hourly cache income. You can get cache through activities, completing challenges, pickpocketing, just plain killing people, etc. Almost everything in the game will give some cache. But the main source will be the hourly income.

The bottom-center option in your hub menu is where you go to claim this hourly income. The bars on the icon will fill over the course of an in-game hour, and once full, will remain full and glow purple. Even though the meter isn't filling any more, the next run of the meter is still filling in the background; this can be seen by claiming your income, after which the meter will often not be completely full.

The amount you gain when you claim your hourly income is based on four things: specific upgrades, activities, targets, and stores. A picture will probably help.

The four sections are, going clockwise from the top:

• Activities: Every activity you complete will increase the amount of income you get per hour. Activities are the blue icons on your map, and generally have three levels of completion (Bronze, Silver, Gold). Stuff like races, Mind Over Murder, Rifts, etc. The completed ones are greyed out, to help you find any you're missing.
• Targets: Every target you complete will also increase the amount of income you get per hour. Targets are the red icons on your map. These don't have levels of completion, and generally vanish when completed. Stuff like Flashpoints, Towers, Virus Injections, etc.
• Store Hacking: Every store you hack increases the amount of income you get per hour. Stores are the green icons on your map. They only have one level of completion, but these stay on your map when finished, since you unlock the option to buy things. Look for a small red lock in the corner of the icon to tell which ones aren't yet complete.
• Cache: This section refers to three specific upgrades you can buy in the "Bonus" section of the Upgrades menu. Each upgrade adds a fixed amount to your hourly income.