[Wayne A. Pflughaupt]

My bass response is diplorable,
I have three separate subs. One in each main and a standalone sub

That may be part of the problem. More oft than not multiple low frequency sources can make a mess of bass response, especially if they are not co-located, and if they are not all identical.

I wonder if it is possible to equalize the subs in my towers apart from the separate sub.

Only if you have line-level access to them, so that you could insert the equalizer in the signal chain.

The BFD does have two ins and outs, right? And are they independently controlled so one could equalize two systems differently?

That is correct.

In your situation I’d try setting the mains to small and using only the standalone sub, assuming that it is a capable one.

Regards,
Wayne