Just wondering if anyone may have an idea about software, that will charge my website users per download that can be integrated into my site.

Or allow them to keep a balance and deduct their downloads from their available balance. Preferably used with a merchant account.

You could do it via PayPal.

You could do it via PayPal.
The problem with paypal is that anyone can chargeback as its not a tangible item. Paypal doesnt protect against this

That is one problem with selling intangible products online as some buyers will just say that they had the wrong product and would ask for a chargeback.