When giving users permissions to specific folders, it applies those permissions to every single file and folder. I do want this but it takes a while for these permissions to be applied to every single file. Is there a different way to give users permissions for sub folders and files within a folder where it doesn't immediately apply those permissions, more like when they open the file, it gives them write access?
No there isn't, but you shouldn't be assigning individual users to shared folders anyway. Use groups and then add users to those groups. Then you won't need to keep propagating permission changes and also keeps you from having a disaster of ACEs in your ACLs.