My Ruby struggles with allergies also...She gets a rash around her inner thigh area between her legs. The doc said to use Benadryl or an Antihistamines from the drug store.
From my experience with leave in conditioners on my Yorkies they tend to get gritty or stiff after a few days. I just use reg. conditioner and just dont rinse it out thoroughly. It leaves the hair soft and doesn't matt.
If you want to prevent matting you really need to groom every few days. Especially the cotton coats, they do matt and tangle way more than the smooth coat Yorkies. But until she looses her puppy coat matting is just going to be a part of life. Ruby is almost three and she doesn't matt or tangle near as much as she did when she was younger. I brush her every other week and a full bath and grooming once a month.
Here is the link to my site on how to groom a Yorkie, maybe it will be helpful:
Grooming - Dawn's Yorkies Ohio