Loose or flaking rust should always be brushed with a wire brush (loose is loose whether converted or not). The remaining rust would still be better to have a rust converter/primer applied to ensure proper adhesion. Any powder residue left over from a rust converter should be brushed, rinsed, or wiped off to ensure the surface is ready to be coated.
Rust converters vary… some add primer and create a primed surface… some (like phosphoric acid) convert, but do not add primer and should generally be washed with clear water to remove any remaining acid before coating. Most auto parts stores carry a sprayable rust converter which can be applied before spraying your bedliner. Duplicolor has a good converter/primer for general application.
NOTE: If using any rust converter, you should start by scraping or wire brushing any flaking or peeling material off first. Since the Diamondback Linings products (Spray Lining and Coatings, or Seal Tite underwater coatings brand) are usually applied with thick layers, you will not generally need to start with a totally smooth surface. Our thick products will smooth irregularities caused by removing flakes or other severe rust.