It is the exact text "separate_category" that you need to change for the additional boxes, keeping upper/lowercase the same in each location. The simplest way would be to just use separate_category2 (adding a "2") for each instance. The category names are irrelevant to this adjustment, though they are relevant to having the sidebox ids and possibly headings match the content.

I haven't used the mod so can't say for sure, but it looks like it may be hard-coded to look for a table named categories, which would fail if your database had prefixes (the table would then be named yourprefix_categories).