Adopted dig crate & accidents in the house

Question
My wife and i recently adopted a male BC Mix and introduced him to our home and our pure bred female Boxer. He has been adjusting well and has not shown too many separation anxiety issues. He has been trained and understands some hand commands as well as verbal commands. We have two major problems though. For one he has for the last 4-1/2 years been crated whenever his family was gone from the house and they brought the crate with him, it now takes up our second bedroom. Our boxer has never been crated except during potty training. We cannot trust him to be out of the crate because he has on two occasions pee'd in the house and since he has never been out of the crate we do not know what he will do. We let him out plenty, we encourage him to go outside an praise him when he does, problem there is he seems to not want to go out when we take him, he is more interested in everything else except relieving himself. He is on a leash when we take him (our boxer is off lead trained and is not on a leash when we take them out) and is very excitable (the second problem) when other dogs and people are around, he looses focus and acts crazy, barking and whining and cannot relieve himself if there are any other distractions.
Last night we took him and our female on a long walk (3 miles) and he pee'd twice on the walk, when we were home we stayed outside for a bit to let him go again and he did not. Since we are trying to break him from the crate we left for the store for 15 minutes and when we came home he pee'd on the side of our bed.
He is used to sleeping on a bed in the past, but we do not let ether dog sleep on the bed, we bought him a nice dog bed and have it next to our bed, the same as our boxer. How are we supposed to discipline him when he pees in the house if his crate is his own private hotel suite? Plus it is big enough for a horse!
He is a good dog, but needs some additional work. Can you help?

Answer
This is not a dog I would "discipline".  He's anxious enough - many herders tend to be reactive and excitable when they have no "career" except "pet".  These are working dogs and need an outlet.  Many of them don't share the same play style as Boxers either, and a BC would not have been my first choice for you, had you asked LOL.  Anyway, if he is reluctant to pee while on leash, it could be that he was scolded while they were trying to housetrain him (so he learned to be fearful of pee'ing in front of humans), or he is too distracted (reactive) and needs some training in that regard to build confidence in his new environment ("Scaredy Dog" by Ali Brown is a good reference, or "Click to Calm" by Emma Parsons - although written for an aggressive dog, the exercises are great for focusing the dog's attention on the handler and NOT the environment).  
It appears that he was not well housetrained by the previous family.  Here's a good basic method, but don't be afraid to use the crate, unless he pees in it:
http://www.diamondsintheruff.com/housetrain.html
You can also elect to tether the dog to you with a buddy leash.  That way, you can prevent any indoor accidents, or interrupt them, and take him directly outside.  BC's are quick learners, so don't forget to REWARD him for going in the right spot.  Good luck.