There are six (6) main types of Currencies in Jetpack Joyride 2:

• Coins - You can earn coins by completing missions, or in any of your runs in any of the game modes. It is the easiest currency to earn.
• Gems - You can earn gems by completing missions, in any runs in Endless mode, Story Mode or Boss Rush. They can be a bit more rare than coins so be sure to grab them when they appear!
• Research Tokens - This can only be earnt by defeating bosses, completing missions or completing orders in your Factory. 
• Vehicle Blueprints - You can only earn Vehicle Blueprints from completing missions or servicing orders in your Factory. Be sure to prioritize upgrading that section of your factory before other sections.
• Marbles - Marbles can only be earnt through playing Endless mode and the are used to purchase stickers from the sticker album. You can only collect 150 marbles per day. This limit resets daily at 9am AEST, so ensure you get all of your marbles before the day ends.
• Materials - These are used to upgrade your badges. Since these can only be earnt through playing Arcade mode mini-games, they are for sure the hardest to get, but you are up for the challenge! Each mini game in Arcade give different rewards and different amounts of each materials. You'll see them ranked from high to low under the mini-game. Consider those to get the maximum out of each game when you want to upgrade your badges.