Can I get clarification of what happens when the status' becomes or changes from Pending to Active. Does it have to do with payment status?
If I am updating the records for Pay later options and the payment is a partial one, should I be leaving the status to "Pending". In addition, should I switch the PAID to "yes" if it's a partial or leave as "no" since a balance remains?
The status is not connected to anything. Once the record is created, nothing will automatically change the status. So even if you update the record to "Paid", the status will remain "Pending" until you manually change it yourself to "Active". So the status change email will not be sent until you manually change the status.
Yes, there are two different emails. They both need to be enabled for them to be sent. So if you intend to modify these two items at the same time, but only get one email... then just enable one of the emails.