Congratulations on your new arrival, Bertie sounds like a proper cocker character (mine eat my Curiosity rose but it didn't kill him
)
It sounds like Bertie's pen gives him too much room at night to allow him to mess and sleep in there, most dogs will try avoid messing their sleeping area so it is good to have a pen/crate... where I think you may be going wrong is the not having a routine with Bertie.
He's only little so may not be able to hold himself all night. Make sure you give him a chance to go out after eating and if he doesn't perform put him out every half hour until he does (you want to be there so you can go over board on the praise so he knows that he's done the right thing
). Try not to feed him too close to bed time either. I also restrict water to mine over night.
I would also set your alarm to get up every 3 hours during the night to let him out. I would try not to go to him when he cries as he'll know he'll get your attention if he does this, but make sure you do see to him regularly. As he gets older you can extend the time between each toilet break (by 10 mins at a time. This may sound tiring but after a couple of weeks he should be able to hold it through the night.
Please take a look at the postings on this site, there's great advice already here and a recommended purchase in 'The Perfect Puppy' by Gwyn Bailey, which should be every puppy owners bible.
Best of luck, Bertie will get there in the end, and don't forget he's only a baby and it will get better!!!