Sounds like you do not have cPanel on the server. The manual backup would be the only way, and you wouldn't lose data doing it this way. It may take a while and slow your connection down due to the fact of how large the database may be.
1) Yes you can - you will lose nothing
2) Again yes, this will work fine
3) I have never heard of this panel, so the only significant change may or may not be just the functionality of using said control panel
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