Dog thinks every room is her patrol room

Sounds like some separation anxiety, the best way to stop her from coming into your room is to contain her to a certain area, either with gates or a crate. just be sure you make that 'her' space and give her reason to enjoy being there. Same for the barking at the windows when you leave, contain her in 'her' space and give her stuff to do there (stuffed kongs ect).

That depends. What do you want her to do instead? You have to replace unwanted behavior with behavior. What do you want that behavior to be?

I haven't known a lot of dogs who are awake enough to wander around at night. How much exercise is yours getting?

I'd be interested in hearing how the 'house rules' were taught, ie; not to come into your room without permission; while you're sleeping; and barking at the windows. How did you train those things?

when we first got her I had no door. She woundered all around the house making it her own. When I first got fed up with it she fought back put I have gained some ground.

As far as what I would like her to do when I leave and come back is I would rather have her just maybe walk around the house and just lay down.

For walking her that is one thing I am working on. She is a pure hound type as I said in the problem statement ("a dog! wait, wait theres a person! wooof wooooooof").

What do you mean 'fought back'?

How much excercise does she get per day?

How much TRAINING do you do with her per day?

I will tell you that baby gates work WONDERS, put a baby gate in the door way of the room(s) you don't want her entering and it will help. I've done this to keep my dogs out of the room with the cat pan, works better than anything I've found OTHER than crating.

I taught Tessa (Great Pyrenees) from the time she arrived home that my bedroom was my Den and she was not allowed in there under no circumstances. We had a XLarge crate for her with a blanket and a woobie (stuffed toy). That was her Den and I didn't go crawling into it; it was hers alone. I had a baby gate installed at the stairs leading to the basement as I didn't want her to fall down them or use them while her bone structure developed. When she was grown she had no inclination to go down the basement. For the cat room we installed a cat door in the bedroom door while she was a puppy.
Because she was with me 24/7 due to my disability she did go to the front window and bark. Definately seperation anxiety. This I couldn't break. She was a guarding dog plus she aided me if I fell or needed help with my balance. For her she felt she should be with me 24/7.

With Choca, she will not even go into her dog house in the pen. Right now she is sitting right behind me on my bed looking out the window dazed almost. Now she is out of the room making sad eyes trying to make me feel guilt, and I feel none.

I would say if your dog is up ALL night something is going on. It may just be stubborn but most beagles LOVE their sleep...then some more sleep...but at the same time they are capable of "going all day" and NEED exercise every single day without fail. Currently, Doug my beagle and I go on a 5KM walk every single day. Some days I am tired and we do 4. Walking fast means this doesn't take me much time out of my day at all, and it's really all Doug is asking for. After a good exercise session, most beagles are content.

If the dog is sleeping all day, then she would have plenty of time to cause trouble all night.

All the suggestions so far are the things I was thinking too.

I would use baby gates to confine her to the area of the house you want her to stay in. I use them and I swear by it. My dogs are not allowed in my kids rooms due to toys and stuff and also that's where the cats like to sleep...I have a gate at the bottom of the stairs keeping them away from the bedrooms entirely. They do sleep in my room at night, but they are shut in and not allowed to wander in and out.

I'm not really sure how you would train a dog to stay out of certain areas when you aren't there without a physical barrier.