Right, go into the initial permissions.yml file and rename the default group that starts there to 'guest' I think it has an option saying build: true
change that to false and remove the permissions for modifyworld.
use the commands from console to set up the ranks:
/pex group member create guest -- this simply means create a group called member which inherits the traits of the guest group
/pex group moderator create member -- same as above but it inherits the traits of member and in turn moderator
/pex group admin create moderator -- I think you get the gist of it by now
You can then add in each permission still through console again with commands (bear in mind you MUST give the first group you want capable to build the permission: modifyworld.*)
use the command:
/pex group member add modifyworld.*
that will give that permission to member, moderator and admin due to the inheritance features you set up.
Now I don't use mytown so I don't know the permission nodes, but if you go to their bukkit page, I'm sure there will be a list, from here on in it will be as simple as typing out every permission using the command above, and changing member to moderator / admin where required.
After this you may want to add a prefix, for example a colour for each group or a part where it tells you exactly what rank each person is:
use the command:
/pex group moderator prefix &9Mod
for example this will make the moderator group members have names which start with Mod and written in dark blue
If you don't want to do it with commands, and instead would rather do it in the yml file, below is parts of my pex file - you can basically substitute in the permission nodes you want - just remember not to use the tab button at all and instead just use spaces.
http://pastebin.com/wwRB2ApK