How many basic SQL statements will you have? Perhaps you could use an expression based precedence constraint to channel the program flow to the correct Execute SQL Task for the need.

As far as distinguising the ?, you simply list your variables in the order in which the ? appear in your SQL. So if your SQL is something like this

SELECT ?

FROM table

WHERE ?

AND ?

You list the variable mappings so that the first one in the list is for the SELECT ?. The second one in the list is for the WHERE ? and the third one in the list is for the AND ?