Is the free item promotional (i.e. a squeeze page, part of an opt-in, or marketing related). Or is it something that is given out as a bonus for a purchasers (i.e. buy $50 worth and get our guide free). I guess my point is this: I am not sure why you are having quantity issues with digital downloads. I sell two e-books through e-junkie and have never had a problem. Considering that I didn't help set up your system, I can only speculate.
My guess (and it is that) is that you are managing the download of your digital products, is that correct? That is, they are being treated by the e-junkie platform as just another piece of physical inventory. If so, you may have to manually enter a number for the inventory (eg 5,000) and just keep an eye on it. When you get low, simply readjust the inventory number.
The reason I asked about the free product and its role is that considering you are giving a product out for free, depending on it's role (bonus with purchase, or promotional give away) and the amount you are giving away, monitoring the "inventory" number could be a pain.
My suggestion would be this: if you are managing the download of your digital products, let e-junkie handle it. It will save you bandwith and eliminate the need for entering an inventory number. I am 99% sure that you can still add them to the same cart as your physical inventory. A little testing should quickly answer that question.
If you don't want to change the set-up for your paid download and your freebee is promotional or part of a squeeze page, then separate it and let e-junkie handle the download for you. Then you eliminate the necessity of managing inventory (wasting time) on something that isn't directly making you money.
I have no idea if this helps, but let me know. It seems like your digital products are being treated as physical items which can be changed fairly quickly.