If you have used a mass import utility to add your old posts to your new blog then chances are that the new posts created in the new blog do not have the same IDs as the old ones. So even if you wrote the correct SQL queries, you would not be able to connect the posts with their correct comments.
However if you do have a away of connecting the old posts with the news ones then the best way to add the comments would be the "WordPress" way, which means doing it by calling iterating old comments and adding them to the new posts via calls to WordPress core functions.
One other alternative might have been installing your new theme to your old blog and then fixing whatever was wrong with it in the first place, but then you wouldn't have to worry about importing your posts and comments somewhere else.