Crate/Pen/Potty Training Dilemma

We have a 7 month old miniature schnauzer named Topper, and we love him endlessly! However, we're having a bit of a problem...

Right before we picked Topper up from his breeder, I was offered a new job where I would work all day instead of half a day as I had been previously. There are no dog walkers in our area and so instead of leaving the poor guy in a crate all day (since he sleeps in it at night as well), we bought an exercise pen that he spends the day in. It worked beautifully and now he never pees or poops in his pen. We've been clicker training him to do his stuff outside, which he does. However, when he's out of his pen he doesn't see a reason to hold it, he'll just go whereever. He doesn't spend a whole lot of time unsupervised outside of his pen, but if you turn your back for a second he'll go right on the floor.

I guess my question is, how do we help him learn to hold it all over the house and not just in his pen or crate? I know it must be our error, I just don't know how to fix it. I know he CAN hold it, I just want to help him learn that he should do it all the time, not just in his pen.

Thanks so much for listening and in advance for any help!

Don't go from pen to whole house. Start with one room and work up from there. You also need to remove all the scents from accidents with an enzyme cleaner.

He sees your house as a territory not a den. You need to actively teach him that it is YOUR den and he is not to soil it.
I would put him on the leash attached to you when he is not in his pen. This keeps you more aware of his actions and you will be more successful at catching him as his is just starting to act like something is going to happen. You need to correct him and then be calm and happy, and take him to the same door you would be most likely to see him go to and then go out with him and reward him for going outside. Use a word like 'outside' as a cue.
You could attach a bell to that door and start to ring it before you go out, praise him and then take him out. Teach him to ring the bell by putting a dab of peanut butter on it and when he licks it, get super happy and take him out.
He just needs more guidance from you and a little more patience and he will be great pretty quickly since he is already so great about his pen.

Thank you so much, both of you! We've been cleaning the spots with Nature's Miracle, which works wonderfully. I should have been clearer as well that Topper doesn't ALWAYS mess in the house, but it does still happen occasionally. After work tonight (and playtime with Toppy) we'll be going shopping for a new, longer leash, and a bell...what a great idea!