Is there any difference in meaning? for example,

"çantamdaki kıtapları aldım" and "çantamın icindeki kitapları aldım"

or 

"O evimde yaşar" and "O evimin içinde yaşar" 

Actually the difference is the same as in English:

- in/at, or

- in/at the inside of

Which would you choose?

My thoughts on the first part:

The first sentence can have 2 meanings

I bought the books that are in my bag. (normal meaning)

I bought the books that are on my bag. (also possible)

The second sentence has only the one possibility

I bought the books that are in my bag.

so both ways mean the same, good to know. Teşekkürler

Well, they both mean that something is inside something else but they are not interchangeable. In English you don´t say "He lives in the inside of my house", you say "He lives in my house." So don´t get too comfortable thinking they mean the same