Photoshop is your best option.. I'm currently working on Back Cards for custom figures, and Photoshop is the only software to use..
You can Google "Action Figure Protective Bubbles" and have a look around.. There are few places that sell.. Or check out eBay and search "Protective Blister Bubbles" which will bring up a fair bit.. There are some on there that are a bubble container that you can seal up, but you can just cut the back section of the bubble off so you only have the main bubble section that you can stick onto your cards.. Also, a lot of people just go to a Dollar Store or something, and buy up cheap figures.. Gives them parts they can use as donor parts to custom figures, but then also they can clean up the bubbles and reuse them for their customs..
You can print straight onto cardboard, but quality isn't the best.. Or do as majority people do and print on glossy paper.. Then cut cardboard to your design (Using template), a good option for this is something like comic book back boards.. Then cut out design on the glossy paper and spray adhesive to back of it and glue into place for front and back of backing card..
Do a search for tutorials on "Custom Action Figure Back Cards" and you'll find a heap that will give you an idea better.. Hope helps..