Storage is only limited by the size of the SD card on the iFly devices. The card that ships with the device is sufficient to hold the entire data set. Aside from download time and any data cap your internet provider imposes, there is no concern with downloading all data.
Similar to the state-by-state selection, once you go through the entire list and select only the charts you want, you can choose to "save selection" and never do it again. From then forward, you can just check for updates, let it download anything that's checked (which it remembers because you saved those selections), and be done. (Don't be concerned if you notice that not everything you checked shows up in the download list when you update. Different products expire at different times, and it will only show the products that have expired since your last update.)
I think it's on the roadmap for the iFly devices (or at least the iFly Connect update tool) to get the state-by-state selection like the non-iFly devices use, but I'm not sure where that's prioritized. Hopefully Shaun will answer that for you.