Amazon Athena will look in a defined directory for data. All data files within that directory will be treated as containing data for a given table.
You use a CREATE TABLE command to both define the schema and direct Athena to the directory, eg:
CREATE EXTERNAL TABLE test1 (
f1 string,
s2 string
)
ROW FORMAT SERDE 'org.apache.hadoop.hive.serde2.OpenCSVSerde'
WITH SERDEPROPERTIES ("separatorChar" = ",", "escapeChar" = "\\")
LOCATION 's3://my-bucket/data-directory/'
You will need to run a CREATE EXTERNAL TABLE command for each table, and the data for each table should be in a separate directory. The CSV files can be in ZIP format (which makes it faster and cheaper to query).
As an alternative to writing these table definitions yourself, you can create a crawler in AWS Glue. Point the crawler to the data directory, supply a name and the crawler will examine the data files and create a table definition that matches the files.