Are you using a membership site? If so, see what recommendations that company has that will interface with the membership program.
Also, have you seen what your hosting company already offers. If they have fantasico, for example, you have a few ecommerce shopping cart options.
Something to consider or maybe you have considered. Kickart has an affiliate program, newsletter program and shopping cart. I beleive it`s less costly if you purchase it by the year? Anyway, the shopping cart is different from a merchant account or 3rd party merchant account like paypal or 2checkout.
As far as merchant accounts or 3rd party merchants, since you`re having reoccuring fees, make sure that any system you purchase, can do that ... legally. And some merchant accounts won`t let you use their services if you`re running an affiliate program. Read the fine print.
My hosting service, well not mine, the one I use, has an shoping cart, affiliate program and newsletter program. No merchant account but they interface with a bunch of them. And I`m considering a company they don`t interface with now, but will set it up for me. However, I`m not sure that I can do reoccuring fees. I have to look into that. Because that would be a good process for me to offer clients and good for you with a membership site.
If you post your specific requirements, I might be able to suggest something. To take money you need two systems - a) shopping cart b) way to take money, through a merchant account or 3rd party merchant account.