Go ask Alex... <G>
To paraphrase a popular sub-culture song.
Anyway, because so many things are hard-coded in the logic to use one default Links.pm file, one Links.Links table, one Links.Category table, etc, the effort required to run two different databases is quite large. Somewhere around January (+/- 2 months) I posted several articles musing about this. I've posted a few since then addressing specific issues in database normalization and keys that _could_ be addressed in a future release to allow multiple "databases" or sets of tables to run so that each sub-tree, category, etc could have it's own "look" and it's own "links" table with it's own field definitions -- such as for classifieds, shopping, links, etc.
Since I'm not trying (aiding or abetting) anyone in breaking the license, and there has been no official word from alex on this issue, I've not taken it any further. But, if you are interested in running two separate "links" tables (essentially databases) from the same script, the key is page.cgi and the use of the dynamic parameter (and others), and using full table names -- as above: Links.Links, Links2.Links, etc.
Please don't ask for any more, either here or privately. You are on your own with this one until GT clarifies the issues.
http://www.postcards.com FAQ:
http://www.postcards.com/FAQ/LinkSQL/