Your Certificate of Marriage will be endorsed at the NSO after your marriage. But it is endorsed by batch maybe like by date of marriage. This procedure is not a problem if you and your spouse are both Filipinos. If you want to be with your spouse in Germany or any foreign country and you need to speed things up for your VISA, you must endorse your Certificate of Marriage immediately and personally at the NSO. In my experience, I went to the local NSO office at Cebu City and submitted the documents personally.
When your paper is endorsed, it will be put inside the NSO database. This means that your document is being archived not just in your local government for example in my case, not just in Cebu but archived in the Philippine documents database or archive. The duration of the paperprocessing usually takes about 1-2 months.