Good advice from Julie.
I'm a qualified veterinary surgeon and that's pretty much the advice I give for dealing with separation anxiety.
The main points are: when you arrive home after leaving the dogs alone, or when you get up in the morning do not give them eye-contact or attention for 15-20 mins - that way they will not associate their messy behavious with bringing you home. Shouting, making a fuss, giving attention etc will serve to re-inforce their behaviour rather than discourage it.
Discouragement should be mimicking an angry pack-leader. A low, growly voice with simple commands. 'No!' etc and, if necessary a sharp, firm (but obviously not violent!) tap/grab to the shoulder. Avoid, prolonged, fussy, high-pitched altercations.
There is a chance that your problem could be due to something other than sep/anx. It could be failure of toilet training. It could be a dietary problem.
Make sure that you don;t feed them too late, you take them out for a decent walk before bedtime and tehn give them time to calm down after the walk before you retire.
Make sure that they are being a fed a good quality, complete food and not getting titbit and the remains of your dinner - as these things will lead to unpredictalbe and varied bowel movements. Chat to you r vet about it - they will recommend a decent brand of food.
If no luck, get them checked by a vet and refered to a behaviourist.
Hope that;s helpful.