I'm not 100% sure what you're not understanding but I'll do my best to break it down for you.
1. Q: " How does the tweak.xm know which game you're hacking"
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A: " When you use your Mobile Terminal and run nic.pl, it will ask you to put the app's bundle ID. (That's how it locates the app you're hacking)
2 Q: " The tutorial states that there's a way to find methods/classes using flex, how do I put them in tweak.xm?
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A: " Basically, if you know how to use Flex and make a patcher that works, you'll be able to take the methods/classes you found and write them your tweak.xm.
IF you don't know to do that, here's a good way to learn :
This Forum is full of great tutorials, read them.
Download ( FlexConverter ) and use it on your Flex patches. It will show you the basics of how a tweak.xm looks when you apply your Flex hack on it.
The most important thing is knowing the basics of coding. Like I stated before, there's great tutorials that will get you started on the basics. I also suggest you download Mimo from the Appstore and use Amuyea's hack here.
Goodluck