I think that once he has finished his first series of shots it would be best to bring him to work with you for 1/2 day if that is possible.
THen he gets a walk at lunch hour and fed, and put in his Xpen at home.
This is how I did it with my troup. I also at times when they got older reversed it up, leave at home until lunch, go home, fed walk, and bring them back to work with me.
At work I used crates and they worked well. You can zip out for a quick pee break at 2 or 2.5 hours and return to work.
Until your yorkie is trained I would not allow him to be free in the office. Most especially as there are so many other dogs there free too.
BTW sounds like you work at an awesome place!!