A battery box does not provide gain, so if your previous settings were working well, there is no reason to change them. Run the DR2d exactly the same as you did prior to the battery box (same mic-input jack, same recording level), except turn off plug in power from the recorder (mic-power / PIP) via a menu setting. The battery box will now be providing power to the mics instead of the recorder. Supplying mic-power from the recorder at the same time will probably not cause a problem or damage anything (capacitors in the battery box should block it), but is no longer necessary after the addition of the battery box. Best practice is to turn it off.
Since the recorder no longer needs to supply power to the microphones, the line-input jack will work, but you probably don't want to be using it for a couple reasons: It's input sensitivity is much lower, so your recorded levels will also be much lower.
It's range of usable input adjustment isn't very wide, so you won't be able to compensate much.
The line-input would be appropriate if you were using an external preamplifier rather than a battery-box. Like a battery box a preamplifier would provide power to the microphones, but also positive gain to bring the signal up to a level appropriate for the line-input of the recorder.