Regarding phone system, everything can be programmed from a telephone using "Flash" commands - usually from X100. You'll need the manual to get anywhere - google will help you find it for free. You can also program via serial/terminal, but no real advantage EXCEPT for backup/restore. There is likely a version of WinDBA for that system - which allowed programming via a GUI interface. For your situation, you're best to program via telephone.
Regarding voicemail, some aspects can be programmed via telephone (recording greetings, light mailbox administration), others via Vodavi "Admin" software with serial connection to VM box.
Regarding "straightening out..." - your issue may be in the phone system OR the voicemail - depending on the exact nature of the trouble.
Overall, it's really a fairly OK system. Lots of features and capability. The battery on CPU is likely at end of life, if it hasn't been changed yet. It would be a good move to perform a system backup via serial, as a power blip with a dead battery can make it so system won't boot successfully.
Good luck