I have put the calibre library under My Documents which I backup between my two machines using a USB drive. This carries all my books and the metadata file across.
Coming to your question, I found that the custom columns ARE carried thru but not the columns' settings. What I mean is that if you have set some columns (custom or builtin) to hide or show; their display order etc. does NOT carry thru. So you will have to set those preferences once in the second machines.
I suspect that the preferences data is held in a different location (under Program Data, I think), but will be a good thing of there is an option under preferences to make a copy of your settings in the same location where the metatdata.db resides.
I have yet to see any program (including paid ones) that are as intuitive and well thought out as Calibre. Great work Kovid, Chaley, GRiker, user_none etc. for creating an extremly useful application.
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