Yay!!! Alternate tuning... One of my favorite topics.
What worked for me, was to always visualize that the low-D notes are on the exact same fret as standard D. I know this seems pretty basic, but it helps to keep that in mind. For example, if you're going to be playing a song in D-minor, play the D-minor scale a few times using the octave:
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--0--2--3--5--7--8--10--12---
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--0--2--3--5--7--8--10--12---
Your brain will quickly adapt to the new tuning by associating the notes this way.