Since base rock shouldn't contain much, if any, organic matter, it's pretty safe to add at any time. If you're unsure how clean it is, you could do a 10% bleach solution, then rinse with water and a dechlorinator until the smell is removed (and then two more times to be safe) but in general, most base rock can just have the dust rinsed off and plopped in like Carey said.
Her method for turning base to live for other tanks is also a great plan, if you ever want a second tank.
Someone stop me! Please! But... not just yet...
55 Gal Tropical FW
55 Gal Mixed Reef