How to determine confirmations using geth RPC.

I am just delving into Ethereum with geth and have figured out how to send and receive ether transactions.

However I am unsure on two aspects of incoming transactions.

1 - How many confirmations is recommended for a transaction to be considered final?

2 - How do I actually determine confirmations with ether? Is it as simple as determining if a transaction is still in the chain (and accessible with eth_getBlockByNumber) after x number of blocks have passed the block that the transaction is in?

2b - What happens to an orphaned ethereum transaction? Is it still accessible from eth_getBlockByNumber transactions? And if so how does one know if it is an orphan or not?

Thank you
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