Thank you so much for your reply. Yes, he is neutered. He was neutered at around 4 months and was also crate trained for 2 years. We had a lab at that time as well and they both were great. Then our lab died, she was 14 years old and we adored her, that is when our Yorkie began to act this way. He started having this trouble with marking and the agression. We thought getting another dog would help but his problems are getting worse. The bassett (his name is Humphrey) does not have these problems. He is also neutered and crate trained. He went from crate to a leash with me in the house at all times and has just recently been "off leash" and is doing well. Humphrey can go on walks well and has had no trouble with housebreaking, despite all the warnings I heard about bassetts! As for Lucky, I am continually spraying and cleaning the carpet with odor remover. I guess I am seeing here we just need to put the Yorkie (his name is Lucky) back in the crate. I am also wondering about the obedience school classes. He is not too old? Thanks for any help, we are desperate!!
Well... I hate to be the one to break this to you but Yorkies are the breed with the MOST house soiling problems bar none.
You did not say the ONE most important point - Is He Neutered?? If not - head to the vet today and have that done ASAP.
Also you know you have two problems: 1) house soiling and 2) protective but uncontrolled aggression.
1) house soiling is a book or at the very least a chapter of discussion on how to correct. But I would start, with Crate Training immediately. (all this assumes you have him neutered!) Google crate training and learn how to establish his schedule and give him psychological security using the natural mimicing of the den. Then while in the house he does not leave your sight (i.e. may not be unsupervised) at anytime if and until he is trustworthy or he is in the crate. this way you can correct "pre-urination" behavior, stop it, guide him to the door, let him out or take him out, wait patiently and praise lavishly when he urinates! This is done consistently for 3-6 months! (sorry I know we are heading into winter but this has been going on for 6 years!). Eventually he will establish a new elimination schedule.
Secondly you need to clean up ALL spots with an enzyme odor remover. Simple Solution is an excellent choice. Use by label directions!!
2) Inappropriate Aggression. Part of this is simply being a Yorkie Male. Like you often see in vertically challenged men, there is a compensation of sorts that happens and they are overly aggressive to make up for their size. He needs to learn what is appropriate "alerting" and what is simply not appropriate and especially what is considered aggression.
This is done by your firm input. First is obedience class! Make him almost an obedience champion. This way he really learns who is boss, he learns to have a confident relationship with you and he learns to listen to you. Then when inappropriate alerting or aggression happens YOU are in control and not him.
I hope one of our behaviorists will join in here and add some more comments, but I've given you several things to start on!
Good Luck.