Food

We love japanese food especially the steam-boat or hot-pot. How do we order tell the waiter we want the type with miso base soup and not clear soup(nabe) or even the type with beef stock taste yummy but we always end up having nabe nabe or sukiyaki!!

AFAIK, miso based nabe is not commonly available exceptin Hokkaido. You should ask the restaurant if it serves miso nabe. If you you can't find it, there is always miso ramen. It is very common.

"Ishikari Nabe" is the most famous miso soup based nabe. As mentioned by Natsuki, it is a Hokkaido specialty. Outside of Hokkaido, you can find it in Hokkaido themed restaurants.

Wildc,

I'm not sure what you mean by "the type with beef stock taste yummy" but do you think it could be shabu-shabu? If so, you need to go to a shabu-shabu restaurant, a place that specialize in shabu-shabu. This is shabu-shabu, by the way.
http://japanesefood.about.com/od/beef/r/shabushabu.htm

Also, isn't "nabe" what you want? What do you mean by "steam-boat or hot pot with miso based soup." Because other than the typical ishikari-nabe, I can think of things like "miso-nikomi-udon" in which you can order in udon or soba noodle restaurants.

"Kaki(oyster) no dote-nabe" is another famous miso based soup nabe. It is originally a Hiroshima specialty but is also available out of Hiroshima, for example at here: http://www.kanawa.co.jp/fune-e-top.htm

A more accessible option to have a variety of miso based soup nabe is going to a "chanko nabe" restaurant, many of which serve its own special chanko nabe with miso soup.