With a mysql instance and multiple databases within that instance is there a way to allocate which database you would like to assign priority to the buffer pool size?
You can configure MyISAM dedicated key buffers. No such buffer scheme exists with InnoDB.
Usually, it is recommended to assign up to 80% of server RAM to the InnoDB Buffer Pool.
Since you cannot prioritize which database or tables can occupy the InnoDB Buffer Pool, all you can really do is create a buffer large enough to hold all InnoDB data.
See my earlier posts on sizing the InnoDB Buffer Pool
Oct 22, 2012: How large should be mysql innodb_buffer_pool_size?
Oct 22, 2012: How much memory do I need for innodb buffer pool? (This was my post on ServerFault that was later migrated to the DBA StackExchange the next day)
Apr 14, 2011: What are the main differences between InnoDB and MyISAM?