Well, when you go into the Burned Tower and go to the basement, they will all scatter around Johto. Raikou and Entei will be roaming which means they will never stay in the same place but Suicune has to be found in these places:
- First, it will be found in the north of Cianwood City.
After you encounter it there, you will shortly find it outside the
entrance of Mt. Mortar in Route 42.
Once you find it here, it will leave Johto and head to Kanto where
you will see it in Vermillion City soon after you arrive.
Next you will see it in Route 14 where it will escape for the final
time to be found outside Bill's House in Route 25. This is where you
Hope I helped!