From this page, looks like you should use charset "latin2" and collation "latin2_croation_ci".
As far as table/field difference, it's just a case where if no field-level collation is specified, then the table-level collation is used, and if none is specified for the table then the database's collation is used.
Also, it's likely that you may need to tell MySQL what character set you'll be using, so after connecting you'll want to submit the following query before doing any other queries:
mysql_query("SET NAMES 'latin2' COLLATE 'latin2_croatian_ci'");