Thanks for your post.
The layout functionlity of the two tools is fairly comparable, but the layout functionlity of SQL Prompt has been more recently attended to.
The layout functionality of SQL Refactor is much more configurable and provides you a greater number of options.
SQL Prompt has less options, but it enables you to do such things as share configuration options amongst developers.
I think the best advice I can give you is to try out the layout functionity of both tools, and see which is better for your requirements.
I hope this is helpful.