First off Welcome to YT
How old is your lil guy? What did your breeder say about his condition? Have never had a pup w/ that problem...however, what exactly did your vet tell you?
I got Meka at 9 wks... I too work full time too 7:30-4:30... when she was a baby, I kept her in a childs playpen in my living room... w/ her bed, water, toys and a pup pad... I use to leave the tv on for her and she was fine. I had to do that for the first month... then hubbys hours were changed and she stayed w/ him during the day... None the less, she was fine (until she learned how to climb out.. lol) You need to keep them in a confined area, until they are fully potty trained - otherwise you'll come home with "presents" everywhere... I dont know that I'd keep him in the bathroom though, maybe you can get an xpen or something like that. Meka stays in the washroom area during the day (its open space) - and I have a baby gate up, so that she cant get out.
Your baby is still getting use to you and his surroundings. So be patient and just keep giving him lots of TLC and he should be fine... And you can try buying some spray (at Petsmart) that goes on the pads... its suppose to help them know to go there.