Dillpill,

Every dog has their own distinct odor, but a strong or foul smelling odor to the urine is a sign of a problem with the urinary tract as is frequent urination (marking would count as urination). While there are additional symptoms such as excessive thirst, straining to urinate, many dogs only exhibit 2 or 3 symptoms. I would at least have your vet check his urine. It may also be related to his allergies as well. If the urinalyses comes back negative for infection, I would concentrate on finding the source of the allergy if possible. You can read up on allergies here:
http://www.nhahonline.com/k9allergies.htm

A lot of dogs have an allergic reaction to corn and wheat and other ingredients in dog foods, so you may want to switch dog foods and use the elimination method described on the following website.
http://www.nhahonline.com/k9allergies.htm

It may take several weeks to see improvement after the change of food. You are already giving benadryl and that is appropriate. There might be a secondary skin condition in addition to the allergy such as staph dermatitis or yeast dermatitis. Staph usually occurs on the lower regions of your pet and tends to have small pimple type bumps. Shampoo containing Chlorhexiderm and/or Oatmeal can help with this condition though it does not cure the allergy. Yeast typically shows as a greasy area that has a sweet musty odor. Sometimes the skin can become inflamed, darker and thickened due to itching. Yeast likes areas such as between toes, armpits and ears. Selsun Blue Shampoo can help with Yeast dermatitis. When shampooing, lather and leave on 15 minutes before rinsing. These shampoos are not meant to be a cure, just a relief.

You may also want to contact a dermatologist in regards XXXXX XXXXX allergy as they may be able to pinpoint the allergy quicker and have a shot developed to desensatize your dog much the same way as they do humans with allergy conditions. I hope this information is helpful to you.