I use wood filler to fill in any imperfections and sand everything down with a fine grit once it is dry. I may repeat that process a few times until it looks acceptable. Then I put down a coat or two of primer and wet sand that while keeping an eye out for any imperfections that you couldn't see without the primer. If its a small imperfection then sometimes you can fix it with simply another layer of primer. Once I'm happy then I put down the spray paint or whatever else I'm using.
If you are having issues with the cut edges of the wood soaking up the primer/paint, you can rub wood filler into the surface with your finger, and then sand it after it is dry. On the non-cut surfaces of the wood you shouldn't have any issue with primer being soaked in if it is sanded smooth.
1998 Civic EX Coupe
Incriminator Audio 6.4
B2 ES6.1i Tweeters & Silver Flute 6.5's
Tantric HDD12 coming soon