By all means poke the vaccum cleaner in there and suck it out before you put it back together but whats got in there is going to get blown out when the engine runs, what little that got in thre shouldn't do any harm as it makes its way down the exhaust. You wouldn't want latge chunks getting clogged in the Cats so a good vaccum out is worth doing. In future plug the openings with some rag or tissue to avoid drbris falling in there.