OK, basically, a CoE is just a document from Japan certifying to the consulate that you meet the requirements to get the visa. Once you have a visa, you don't need the CoE. (Keep it just in case something happens with the visa, but don't expect to ever have to use it again.)

The visa gives you a fast-track to get landing permission when you arrive in Japan. Once you've gotten past immigration at the airport, your visa is no longer relevant: what matters now is your "status of residence," which is your immigration status for internal purposes. Your status of residence is calculated from the date you arrive in Japan... on a work/student/spouse visa it's usually 1 year, or 3 years if you're lucky.

If you're staying for more than 90 days, you have to register as an alien with the local city hall, and get an alien registration card (aka gaijin card). If you leave the country without a re-entry permit, you have to give up your gaijin card. Even if you keep it (which is easy--just say that you lost it), immigration will send a message to city hall telling them to delete your existing alien registration and send the files into a vault at the Justice Ministry... so you have to re-register when you go back, or else you won't be documented anywhere as a resident.

A re-entry permit keeps your alien registration intact and simplifies the procedures when you come back to Japan. You still have to fill out the usual landing cards, but no additional paperwork is required, and the immigration officers have very little discretion to deny you entry, whereas if you enter on a "mere" visa they can deny you entry for any number of reasons. (BTW, you get a re-entry permit at the immigration bureau, not the ward office. If you're in Tokyo this means schlepping over to the Customs House way out in the middle of nowhere on Tokyo Bay...)

Having a "multiple entry visa" just lets you enter Japan as many times as you want during the term of the visa, with a new status of residence each time. It won't keep your alien registration intact. Assuming you have a one-year or three-year status of residence (the usual durations), you're better off getting a re-entry permit: besides the not having to re-register part, the re-entry permit is valid for a year after you ARRIVE IN JAPAN, as opposed to a year after the date of the visa. If it's a tourist visa, this doesn't really matter because you probably won't be registering as an alien anyway (unless you want to open a bank account or something).

Re that last question, as far as I know, a spouse visa remains valid for the stated duration even if you get a divorce. You just can't stay beyond the term of the landing permission unless you get your status changed to something else (e.g. by applying to renew as a working stiff rather than as a married stiff).

That's about all I know about this subject but I hope it helps you figure it out...