How is energy and waterconsumption data collected?

MPR 6's methods of reporting continue to evolve... You are correct that teams report total building energy and water. Teams are expected to be proactive on a monthly basis for this data reporting. I am not aware of notifications from USGBC/GBCI for the USGBC approved data template option. Theoretically USGBC/GBCI would be in touch with the team's project administrator from LEED Online if there data is not being provided. Personally I am not aware of users being notified but my teams have always complied using Portfolio Manager (third party data source) for reporting. And as the project team administrator, I follow up with my teams annually to ensure the data is being reported as required. If you haven't already, check out the Sample Forms for Project Information Form 1 (PIf1) - https://www.usgbc.org/node/10158425, which outlines the requirements for all MPRs including MPR 6 under #6. A project’s Owner commits to providing five years of energy and water data as part of the PIf1 form. This is why I, as the team's Project Administrator, never complete the PIf1 form and instead have my team’s owner complete it. In addition, the Language and Resources tabs for MPR 6 in the Credit Library are useful - https://www.usgbc.org/node/1731548. Also, consider checking out the FAQs on the USGBC's website: 

1. https://www.usgbc.org/help/i-am-having-trouble-choosing-option-comply-mpr-6-requirements-can-you-explain-differences - and be sure to use your browser's search function to find other MPR 6 FAQs on that same page.
2. https://www.usgbc.org/help/how-do-i-share-access-usgbc%E2%80%99s-portfolio-manager-master-account-if-i-chose-option-1 - and in case you're going to use Portfolio Manager as your reporting tool, be sure to use your browser's search function to find other Portfolio Manager FAQs on that same page.

Read about termination in LEED Online’s LEED Certification Agreement - https://www.usgbc.org/resources/leed-certification-agreement, which all teams must sign.  The LEED Certification Policy Manual - https://www.usgbc.org/resources/leed-certification-policy-manual- states “GBCI retains the right, in its reasonable discretion, to revoke LEED certification from any project where it is denied access to, or for which it is not provided with, energy and water use data on an ongoing basis after LEED certification is conferred, as is required.”