Re: Can I use LVDS (in and out) from those banks which is powered from 3.3V?
You'll also be interested in the specifications/text just above Table 12 (top of page 16). To answer your initial question in short though, the Bank 0 DIO (DIO 0-15) can only be used as Single-Ended 3.3V.
As for the rule checking part that Spex mentioned, this is what will happen if you try to choose LVDS for Bank 0.
In general, as you're developing your pinout, I would recommend testing that pinout with the sbRIO CLIP Generator. Because we have rule checking in place, it will help make sure you are properly using the I/O from the board and help catch any issues before investing time in layout/fab/testing. Also, as an added benefit, you'll already have your socketed CLIP developed for the LabVIEW project.