After getting CoE and tourist visa

Hi, my bf is is waiting for CoE and work visa, but he's in a complicated situation now.

When you get CoE for company, you'll need to go to Japan with tourist visa and CoE within 3 month to proceed with paperwork of work visa at Japanese embassy, right?
Actually he already spent 180days (90days + 90days) of tourist visa in Japan this year, so he's not in Japan now and he can't come back to Japan with tourist visa anymore...what should he do after getting CoE? I was wondering is it possible to ask his company to do apply work visa instead of him?

I'm Japanese and tried to find out the way but no information about it.
If anyone has related experience or advices, plz let me know.

Thank you in advance.

I assume your non-Japanese boyfriend is outside Japan now.
When he receives the CoE for his work visa (the employer in Japan will send it to him), he goes to the Embassy of Japan is his country and use the CoE to apply for the visa.

Thank you so much AK, it's really helpful.
I hope it works soon

If he's outside of Japan and getting his COE issued outside of Japan, you don't come to Japan on a "tourist visa" as you're not a tourist any longer. The point of the COE is to turn that into a work visa or the appropriate visa to enter Japan to live under those conditions. If he came as a tourist before and stayed for a long time, he's enter under a new category, so it should be fine.

When you get CoE for company, you'll need to go to Japan with tourist visa and CoE within 3 month to proceed with paperwork of work visa at Japanese embassy, right?
No - false. As @AK states, front up to your local Japanese embassy with the COE and apply for the visa - takes a few days.

Actually he already spent 180days (90days + 90days) of tourist visa in Japan this year, so he's not in Japan now and he can't come back to Japan with tourist visa anymore
So? Every visit under the tourist waiver program he gets another 90 days. There is no limit to the number of times or number of days a temporary visitor can stay in the country as long as you leave before the expiry of the permit. Note, there is no "tourist" visa, and under the waiver program it is a permit, not a visa (just to be technical).