Is it something people might buy a good amount of? You could look in to something like a credit on the site (IE the user can add credit in $5 increments). Or you could bill when they customers has gotten to $X (this is risky in some cases). Wouldn't it be easier to just get creative with the business model, rather than try to deal with the hassle of $0.99 coming over and over again with little remaining when you receive it?
