I had rust in the gutters too and a couple of bubbles just above.
Personally for the vehicles body I wouldn't just spray rust converter on and paint over and hope for the best.
I removed the rust entirely using grinder until every single sign of rust was gone. I had to cut through the entire panel exposing the inner panel of the roof and then applied rust converter inside the gap to ensure nothing will start up again.
Then clean and bog it all up, sand back, apply primer and paint.
Have a look below for a basic post about what I did....
http://www.nissanpatrol.com.au/forum...ly-here/page33
I am fixing my trailer this way by just rust converting and applying primer, paint, etc but It's only an old trailer. You would hate to have it bubbling back up again on your vehicle a few months later.