The undress function will always remove everything you currently are wearing except items in your hands (sword, shield ...).
When you attempt to dress UOAssist will only put on the items in the list IF nothing is currently in that 'place'. Meaning if you setup to dress with a feathered hat but were already wearing a plate helmet the hat would not be put on.
Setting up what items to dress with is much like setting up arm settings. Have your character put the items on and then select which 'slot' (main, alternate, ...) you want to set and push the button 'Save what is currently being worn'.