Create new database for each webapp/environment:

CREATE DATABASE new_db;

GRANT ALL PRIVILEGES ON new_db.* TO 'some_user'@'localhost' 
IDENTIFIED BY 'somepassword' WITH GRANT OPTION;

FLUSH PRIVILEGES;

Get approximate disk usage by table in your database:

SELECT table_name, (data_length+index_length)/power(1024,2) tablesize_mb 
FROM information_schema.tables 
WHERE table_schema='shoptool' 
GROUP BY table_name 
ORDER BY 2 DESC;

See what table engine (MyISAM, InnoDB) each of your database tables is using:

SELECT table_name, engine
FROM information_schema.tables 
WHERE table_schema='your_db_name';