After waking them in Ecruteak City they will run off, it's then a case of being lucky to encounter them as you travel through Johto. Once you encounter one of the dogs you will be able to track them in your Pokedex. Don't try to enter the exact route they're on as they will flee the moment you enter the route to a new location so it's a case of predicting their path. I found Mahogany town and the Route to it's Left useful for being at the right place to encounter of one of the dogs a second time.
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You can find Lugia, the legendary dogs/ Suicune, Enti, and Raichu, and I think Ho-Ho
yes if you can find them
There are 3 ... you can get the Legendary Bird Pokemon ( HO-OH ) you can find it at the ten tower ... you must have a rainbow wing to enter the tower. but the other 2 Legendary Pokemon i don't think you can get them.
The story line in crystal is a little longer and you encounter the legendary Pokemon in a different order than gold and silver. The mascot in Crystal is Suicune, one of the three legendary dogs, and can be caught in the Bell Tower after many encounters in the region. Gold and Silver's mascots are Ho-Oh, the guardian of the skies, and Lugia, the guardian of the seas. There are also some differences in the wild Pokemon. An example is in Gold, you can find Spinarak, while in Silver, you can find Ladyba.
When you first find the 3 legendary dogs, they are in the basement of Ecruteak's Burned Tower.