Hi Cani1
Some dogs are just very vocal and make it clear that they are bored/want your attention/have an unsatisfied desire for something. This is the sort of whining you might get if you're eating your breakfast and your dog is with you, waiting for his walk. Unfortunately, there's very little you can do about this sort of whining. I do believe that dogs can be taught not to bark - but they seem to be much less aware that they are whining, it just seems to be an unconscious thing a lot of the time and I think it's largely genetic.
It's v hard to know if you have a dog with this sort of 'bored' whining or a dog which has SA, from your description. But barking the house down in his crate suggests SA.
The first step of crate training is NOT TO LEAVE THE DOG IN THE CRATE! The dog must be absolutely fine in the crate for any length of time with you sitting right next to it, before you begin to leave him in there. I'd suggest you revisit the various crate training steps without leaving him. In short:
1. Leaving crate door open and hiding treats in there when he's not looking, so he believes it is a magic treat producing place - do this for several days. NEVER close the door at this stage. Make sure the blankets and bed in there are very comfy though so he might decide to lie down in there of his own free choice - still don't close the door. The crate should be in a busy family room, not in an unused utility room - it should be at the centre of family life.
2. Feed him his meals in the crate, putting the bowl in there at the back and closing the door whilst he eats, then IMMEDIATELY opening it when he finishes. Do this for several days.
3. Now comes the first time you shut him in. Make sure he is well-exercised and tired. Fill SEVERAL kongs with peanut butter or soft cheese spread, put them all in the crate and SIT NEXT TO THE CRATE. Do NOT leave him. Watch a film on TV, sitting right by the crate for several hours. Do this until he is fine with it. This might be several days or weeks. NEVER leave him in the crate during this time.
Only after that can you begin the separation training elements, which I won't go into here...
There are 2 parts to crate training: A) getting the dog used to being in the crate and happy in that confined space and B) getting the dog used to your separation from him. Too often owners combine these two things at once. Then when the dog barks, you've no idea if the dog is barking because he doesn't like the crate or because of the separation from you. You need to ensure the dog likes the crate first, so you can then KNOW that any later barking is due to separation and not to the crate.
Good link here:
http://www.ddfl.org/sites/default/files/crate-train.pdf