First option is when you are inserting the bolt, select the push pin on the Insert Component box. If the bolts you are using are from the toolbox or setup with mate references you can go from hole to hole dropping components in.
Otherwise you could do a component pattern. If the holes are all in a row use the linear pattern of if they are in a circle the circular pattern. Otherwise you might be able to use the Feature Driven Pattern. I haven't used it much, but I have used this where the hole wizard generated the holes on the part. Insert the first bolt into the first hole, do the Feature Driven Pattern, select the bolt and then select the hole on the part for the "Driving Feature" and it should throw bolts in all of the holes generated by that feature. There might be other ways to utilize the feature driven pattern in case you didn't use the hole wizard, but I haven't used this feature to much to know for sure.