You can add the Reefer Rock directly to your new aquarium (it won't be live but your live rock will seed the new rock fairly quickly). You can consider the rock as neutral. I only recommend a quick rinse of the Reefer Rock prior to putting in the tank.
As for trying to prevent bringing hitch-hikers to the new tank - this is going to be somewhat difficult. You can try putting each piece of live rock through a carbonated water dip. You dip for 30-60 seconds each piece in a bucket of carbonated water - a lot of the hitch-hikers will evacuate the rock quickly but you will not be 100% successful.
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A solid foundation leads to a happy, healthy eco-system!
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