I used to use Bodyshop's crayon concealer, followed by the creme concealer from Stage, now I'm using the liquid concealer by Amazing Cosmetics, and it's amazing! Covers my dark eye circles and spots really well.
Try using a makeup primer and a good liquid foundation. Makeup Forever All Matt primer and Velvet Mat+ foundation are quite higly raved about. I find Estee Lauder Double Wear foundation works wonders, and Clinique Superfit (but I realised it's been discoutinued...)
Depending on my mood! I will use my fingers, or a damp sponge, or a flat foundation brush, or a stippling brush. Most of the time I used my fingers as I am lazy
There are loads of primers to try. I would recommend trying some from Make Up Forever, She Uemura UV Underbase, Boots no.7, Too Faced Primed and Poreless, Urban Decay has some primers/bases too.