.. so you can at least get data for those TFs that have been characterized thus far.

Yes bobf, my intention is only to extract already characterized TFBS from TRANSFAC database. I'm not looking for new TFBS of fruitfly.

Go forth and parse (the TFBS modules may help you here)

Having looked at the TFBS module. I can't seem to find a method that allow me to pass the query "fruitfly" or "drosophila" and then returning the:

1. already characterized TF and their binding sites (BS),
2. their respective coregulated genes, and
3. the location of TFBS location/position in the genes.

all from TRANSFAC database. Perhaps a good example of database that has this all this in straightforward manner is SCPD (database for yeast). But TRANSFAC seems to be more complex for doing this task. Any advice on how can I make use of the module as you suggested?

Certainly I don't expect a silver bullet method from TFBS module that return all that. But at least a method that allow gives me a starting point to achieve that tasks above.