Aussie biting

Question
Hello and thank you for all the great advice over the last two years since I have got my Aussies...usually somebody else has already asked what I need to know so I haven't needed to ask personally.
I have a male tri who is nearly two and a female tri of roughly the same age. The male cocks his leg everywhere in my house. I am an experienced dog over but have never had a male before and its driving me nuts..is there anything we can spray or use to help this?

Secondly and more importantly my female, who has always been "growly" has now taken biting tall men who come into the house. I know that the tall men thing is because our vet (who she is petrified of ...my husbands fault not the vets.. he is a kind vet) is tall and I know that she is super protective of me. She sort of nips coat and arms...not really ferocious teeth bearing but as it has already progressed from growling I am frightened it will get worse. I have started agility with her which is doing us both the world of good but it seems to be heightening her already super loyal over protective thing for me. The male beats up on her all the time and she always sought solace from me ...I don't know if thats anything to do with it aswell.can normal training sort this out as I am scared she will injure someone and have to be put down or is clicker training better? She is obedient otherwise.Should they still be fighting at two? Thanks

Answer
If they are play fighting, and there is give and take between them, that is normal.  If there is genuine sparring with injury and they are two years old, that's more serious.  Your male needs to be neutered if he isn't already, and that may stop the marking (although some males continue it if they have been neutered late).  A dog that has "stranger aggression" or fear aggression is likely that way due to a bad experience, inadequate socialization during the critical period (8-16 weeks), or because of genetic tendencies.  The latter would suggest a dog that should not be bred.
Agility is a good confidence builder, but may not preclude her from the cheap shot nipping behavior.  You are correct to worry that a dog that grabs and nips may get worse.  One thing you can do is to test her thyroid (have your vet send the sample to Hemopet and do the full panel).  The first thing you always want to do is rule out a physical cause.