The tool to use depends on the application.
For coating: Use a plastic squeegee, plastic epoxy spreader, disposable brush, or a short nap (1/8") epoxy/solvent-safe roller cover.
For cloth lamination: Use a plastic epoxy spreader, disposable brush, or laminating epoxy rollers.
For bonding (commonly a thicker epoxy, or epoxy that has a thickening agent added to it): Use a glue brush, acid brush, chip brush, or notched spreader/squeegee.
For fairing: Use a plastic squeegee, plastic epoxy spreader of an appropriate length, putty knife, or other tool that is contoured to the surface.
For injecting epoxy: Use an epoxy syringe, pipette, or acid brush/glue brush.