During the Bitwala wallet creation, three keys are generated because the wallet is a so-called "2-of-3 Multisig" wallet operated by BitGo. You write two of the keys down on your paper backup.
Key #1 is 12 words (seed 1 / master key), which is also stored password-encrypted at BitGo. You absolutely need it if you forget your password or Bitwala goes offline.
Key #2 is also 12 words (seed 2 / backup key) and exists only as a seed on your paper backup. You really need these 12 words if you forget your password or Bitwala should go offline.
Key #3 is stored invisibly for you at BitGo.
A transaction is as follows:
1) You generate a transaction
2) We request your encrypted key #1 from BitGo
3) You decrypt it with your password
4) You sign the transaction with key #1
5) BitGo checks the operation (e.g. unusually many transactions from this IP) and co-signs with key #3
So key #2 is not used in a normal transaction.
If Bitwala (which we do not hope) should be offline, you can use Key #1 and #2 (Seed 1 and Seed 2) to "import" your Bitcoin elsewhere. It applies what Andreas M. Antonopoulos says: "Not your keys? Not your Bitcoin."