Ah... the Whitman mess. It depends upon the series/issue really. Western's "imprints" are not imprints in the modern sense, but instead publishers. See the following post for a detailed summary of Western's history:http://www.comicbookdb.com/forums/viewtopic.php?f=2&t=1060#p4016
Note that the last paragraph refers to the Whitman reprint problem. As you've found, there hasn't been a lot of consistency regarding this in the database. Following DarthSkeptical's advice, Whitman reprints should probably be their own individual titles with reprint links to the Marvel/DC/Gold Key issues within. On the other hand, if its an original Whitman issue, and follows numbering continuity from a Dell or Gold Key series, then it can be indexed under the same title (assuming the indicia title remains the same) with an appropriate title note about the series' publishing history.
Western's publishers were so prolific for such a long time.. It's a big mess that needs a thorough cleaning. Less confusing problems seem to keep getting the priority for some reason.