I created Domtool configuration for my domain and ran the domtool program on it, but my domain doesn't work at all.
Did you use the domain directive instead of the dom directive? domain is the primitive directive, where you must specify all details manually. If you're using domain and haven't listed the right nameservers manually, then your domain will definitely not work. Instead, use dom, which includes our current idea of the proper base configuration. We can change this later without any need for you to change your configuration.
There are various other ways that you could run afoul of this general problem, which is that our DNS servers won't answer any queries for zones that don't have some nameservers set. This behavior comes from BIND.
I changed my Domtool configuration file, but the changes don't seem to have taken effect.
You must always rerun the domtool program to publish changes. You can run it on an individual file, or you can run it without arguments to reload all configuration in your ~/.domtool directory.