1) The Global Cemeteries Project is split up into subprojects based on country, and then in some countries split up further by province, state, etc. Each subproject keeps track of which cemeteries have been photographed by its members. Eg. here's the progress page for my provincial project, Manitoba Cemeteries.
2) Keeping a cemetery up-to-date is a challenge faced by all groups that attempt a project like this. What I've been doing is recording when I photographed the cemetery. That way, in the future, I or someone else could go through the cemetery faster just looking for deaths after that date.
3) You don't need anyone's permission to photograph tombstones in a public cemetery, but you might for private cemeteries.
4) Once we have the pictures, we transcribe them into a table on a free-space page (eg. St. Jude Church Cemetery) and upload the pictures to WikiTree profiles. If you look at the table in my example, you'll see a couple of the names have links to profiles I've created for them. The photos of their tombstones are uploaded there.
I hope that helps! :)