If you use the auto feature then yes, I believe it would image both partitions. If you leave that unchecked, then it should let you select which drive you want.
As far as using lightning for windows, I believe more testing is needed.
I have been playing around and was easily able to image USB drives that were FAT and usable by windows.
Lightning uses standard ASR (Apple Software Restore Images) and standard DMG files.
If you made a dmg of something that happened to be NTFS and have Windows Installed on it. In theory it should work. If these were Apple computers that's not so bad becase TDM will make the drive mount, IF you are talking about a DELL, HP, or other laptop, I would think a sled or something where you removed each HD would need to be done.
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