Mysql covering vs composite vs column index

In the following query

SELECT  col1,col2
FROM    table1
WHERE   col3='value1'
  AND   col4='value2'

If I have 2 separate indexes one on col3 and the other on col4, Which one of them will be used in this query ?

I read somewhere that for each table in the query only one index is used. Does that mean that there is no way for the query to use both indexes ?

Secondly, If I created a composite index using both col3 and col4 together but used only col3 in the WHERE clause will that be worse for the performance? example:

SELECT  col1,col2
FROM    table1
WHERE   col3='value1'

Lastly, Is it better to just use Covering indexes in all cases ? and does it differ between MYISAM and innodb storage engines ?