KC,
Both issues can be addressed under the phone configuration page. You can add a second/third etc line there as well as under the DN configuration extend the ring no answer timer.
You can also extend the RNA timer under system parameters but that would be a global change affecting all the phones on the cluster. If that's what you are after then you are better off changing it in the system parameters.
it can be very frustrating trying to administer a system that you don't know. However once you get used to it you will see that it is easy and extremely powerful. You best place is cisco.com for all administration enquiries. All guides and docs are open to everyone and easily accessible.
I am attaching a link that should get you started:
This is a complete administration guide.
As far as the voice mail issue goes you need to understand that it is your email server that stores the messages and not unity itself. When a message is deleted it is gone, whether you delete it from the phone or your email client on your pc.
It sounds to me that the users were not trained properly on how their new unified messaging works. I would think that if the users are informed that once they delete a message they cannot retrieve it, it will be understood.
Why would you delete a message and then expect it to be there anyway?
I would suggest that your company provides you with formal class training if they expect you to support the new system. I can't imagine they have the expectation that you will be taking over without training just because you have a AVAYA pbx background. Every system is different and mastering one does not make you an expert on any other.
You have the foundation to learn it, you just need the tools.
good luck and the folks on this site are always willing to help out and answer questions.