I have an intake that has the egr plate on it, but has a hole on the bottom of each runner, will exhaust gas get into the intake????

not if it has the egr block off plate is bolted to the intake

if you are worried about those "jet" holes, they can be tapped for 1/4 or 3/8 pipe[i forget which size]and use a hex plug to fill 'em. if there is a big "jet" hole i one runner, you will have to detirmine the size and tap accordingly for a larger pipe tap size, or a normal bolt size. if using a bolt, machine the head to approximately 1/8" thick to minimize flow restriction.