Your Recoll configuration always defines a main index. This is what gets updated, for example, when you execute recollindex.
You can use the search configuration tool to define additional databases to be searched. These databases can be made active or inactive at any moment.
The typical use of this feature is for a system administrator to set up a central index, that you may choose to search, or not, in addition to your personal data. Of course, there are other possibilities.
The main index (defined by your personal configuration) is always active.
The list of searchable databases may also be defined by the RECOLL_EXTRA_DBS environment variable. This should hold a colon-separated list of index directories, ie:
export RECOLL_EXTRA_DBS=/some/place/xapiandb:/some/other/db