Night time... barking and messes

Question
Our 6 month old is mostly well behaved, except at night. There are two issues
(although they might be related).

We keep our puppy in the laundry room at night. We do not crate him, he has
a comfortable be and a toy or two outside. We place down two pads at night
so he has lots of area to relieve himself if need be.

BARKING:
Normally he starts barking at some point at night. He starts sometime after 3,
and goes until I get up at about 6. At one point we used to get up to walk him
at these points thinking that would resolve his issue, but it really just made it
worse. We tried to discipline him in the middle of the night, but that had no
real use. We have praised him greatly when he made it through the night
without barking, but I think that has only happened twice... not much to
praise.

We tried putting him in a crate, but wails hideously in this case (and soils in
the crate... not pretty).

I am certain it is due to separation anxiety. He is around people 100% of the
time when not sleeping ( I work from home ). However we feel strongly about
wanting him to sleep by himself. This behavior really annoys us. We are afraid
of guests coming, I I really dislike waking up angry because of this.

POOH on pads
He much prefers to go pooh outside, which is fine with us. He will even go on
really nasty days. At night we have some problems however.
He often (not always) misses the pads. Sometimes the pooh is not ever close.
The pee is always on a pad.
We put 2 pads out since I suspected he doesn't like a crowded pad.
We always walk him right before bed, and he always relieves himself then. His
also does not eat in the later part of the day (normally later afternoon he is
done).

Most of the time the pooh issue is slightly inconvenient, but I can't
understand why? It also makes us not comfortable leaving him unattended
during the day.

Any perspectives on what we could do? Especially with the barking.

thanks

Answer
Hi, i hope you are well.
the barking is a tricky issue but you have to be firm but fair there are a few tricks you could use but the main thing is to be firm and ignore the behaviour do not get up to him unless absoloute nesecarry the seperation issue will be a key factor. Maltese love affection and attention and they love being with their owners all the time. A trick you could use is sleeping with a blanket then putting it in his basket the next night as it will have your scent on it to help comfort him.
Also you can buy those bean bag soother toys that you can warm in the microwave the heat reminds them of sleeping next to their mother and again soothes them. another little trick is a portable radio that you could put on low for him when he wakes up thisx wll help comfort him as the noise will be a constant company.
As for the pooh issue i believe that he may be getting a little confused as he usually goes outside and he doesnt know where to go now my suggestion would be to try and eliminate the pads completley at six months he should be able to hold his own until morning but again accidents will occur until perfection is acheived.
I really wish you good luck i cant relate at present as i am a push over and my maltese come to bed with me but i appreciate that you have to have boundaries and night is your time for yourself  so good luck and please let me know how you get on.
Thanks