It's not too late, but it does take work, patience, and consistency.
How long have you all had this dog? If your wife and son adopted it while you were deployed, that means they had it awhile when you were gone, and you've been back long enough to feel inconvenienced by it, so, it seems like it's been in your home awhile.
That just means that your wife, son, and dog have developed a routine already, and part of training it to have manners and be potty trained is setting up NEW routines. Changing routines takes lots of patience, because dogs don't learn overnight.
For potty training:
- Potty training is more about what YOU do than what the dog does.
- PREVENTING accidents is the key.
- You have to start as if you have a new puppy. Take the dog out every hour (not because he can't hold it longer, but because you are setting up a new routine and laying a foundation for what you want in the future. Taking him out so often will help PREVENT accidents.
- When you take him out, you have to differentiate between play/exercise time and potty time. Potty time should be boring. Take him out on a leash, say the same potty words each time, and give him lots of praise the instant he starts to pee/poop. After he's finished, give him a treat, while you're still outside.
- Supervise him super closely. Yes, it's a hassle to have to keep your eyes on the dog, but, if you PREVENT accidents by watching him, and rushing him out when it seems he has to go, you will have him potty trained faster.
Don't scold or punish accidents. When he's learning what you want, if you punish, it may end up making him afraid to pee/poop in front of you, or at all, which will cause problems when you take him out.
Really, it's all about prevention. The more you can prevent accidents and redirect him outside, the sooner he'll come to learn that outside is the place for peeing /pooping.
If you don't want her on the furniture, you have to teach the command "off", or something similar. You teach it to her as if it was a trick. Use a treat, point to the floor (when she's on the couch), look at the floor, when she gets down to get the treat, you praise her and say "good off!".
This takes practice, as if it was a trick, or command like "sit".
If the dog happens to be smart and decides to get up on the couch again, so that you will tell her "off" and she gets a another treat, try this: after she gets "off" when you tell her, give her a few other commands or activities. The more time/separation you put between her being on the couch, the less likely she'll try to get right back up so you'll say "off" again and she gets another treat. You want to take her mind off being on the couch.
And, if she isn't potty trained, don't allow her on the bed or couch unless you know she's just peed and pooped and is "empty".
For barking, it may be to be let out, or it may be out of boredom. Dogs should be walked daily, at least once a day for 30-40 minutes. Playing in a yard isn't enough. A walk is also mentally stimulating, and being mentally stimulated is tiring, too. So, a walk is really twice the exercise, physical and mental.
Training will also tire her out.