Are you sure the appearance tool of AFT is for settlers, too? I thought it is for followers.
I don't know a mod for changing settlers look, I would be interested in it. You could open console, click on the settler to see his refID, and use the showlooksmenu command to change his look. I did this some times, with mixed results. Partly it worked for long, partly not.
To change weapons and clothes/armor for settlers is easy, as said. Talk to them, put the item into the settler inventory and press "T" to make him/her use it. If you give a gun to a settler, you need to put ammo for it in the settler's inventory (1 round is enough, except for missile launcher or fatman; advice: don't give missile launcher or fatman to a settler!!).